From af57b416b0e2e4149f141db2ddce8e7aa9d0308c Mon Sep 17 00:00:00 2001 From: mathiasg Date: Mon, 22 Jan 2018 10:41:22 -0500 Subject: [PATCH 1/5] enh: update zenodo entries --- .zenodo.json | 413 +++++++++++++++++++++++++++------------------------ 1 file changed, 220 insertions(+), 193 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index a625eb2669..042121454a 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -11,9 +11,9 @@ "orcid": "0000-0001-8435-6191" }, { - "affiliation": "The University of Iowa", - "name": "Ellis, David Gage", - "orcid": "0000-0002-3718-6836" + "affiliation": "Independent", + "name": "Ziegler, Erik", + "orcid": "0000-0003-1857-8129" }, { "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", @@ -21,19 +21,32 @@ "orcid": "0000-0002-5866-047X" }, { - "affiliation": "Independent", - "name": "Ziegler, Erik", - "orcid": "0000-0003-1857-8129" + "name": "Burns, Christopher" + }, + { + "affiliation": "The University of Iowa", + "name": "Ellis, David Gage", + "orcid": "0000-0002-3718-6836" }, { "affiliation": "University of Iowa", "name": "Johnson, Hans", "orcid": "0000-0001-9513-2660" }, + { + "affiliation": "Klinikum rechts der Isar, TUM. ACPySS", + "name": "Manh\u00e3es-Savio, Alexandre", + "orcid": "0000-0002-6608-6885" + }, { "name": "Hamalainen, Carlo", "orcid": "0000-0001-7655-3830" }, + { + "affiliation": "MIT", + "name": "Jarecka, Dorota", + "orcid": "0000-0003-1857-8129" + }, { "name": "Yvernault, Benjamin" }, @@ -43,37 +56,35 @@ "orcid": "0000-0002-6533-164X" }, { - "name": "Burns, Christopher" - }, - { - "affiliation": "Klinikum rechts der Isar, TUM. ACPySS", - "name": "Manh\u00e3es-Savio, Alexandre", - "orcid": "0000-0002-6608-6885" + "affiliation": "Florida International University", + "name": "Salo, Taylor", + "orcid": "0000-0001-9813-3167" }, { - "affiliation": "MIT", - "name": "Jarecka, Dorota", - "orcid": "0000-0003-1857-8129" + "affiliation": "Department of Psychology, Stanford University", + "name": "Waskom, Michael" }, { - "affiliation": "Florida International University", - "name": "Salo, Taylor", - "orcid": "0000-0001-9813-3167" + "affiliation": "Developer", + "name": "Clark, Daniel", + "orcid": "0000-0002-8121-8954" }, { "affiliation": "Shattuck Lab, UCLA Brain Mapping Center", "name": "Wong, Jason" }, { - "affiliation": "Department of Psychology, Stanford University", - "name": "Waskom, Michael" + "name": "Loney, Fred" + }, + { + "name": "Madison, Cindee" }, { "name": "Modat, Marc" }, { - "affiliation": "National Institutes of Health", - "name": "Clark, Michael G. " + "affiliation": "MIT", + "name": "Goncalves, Mathias" }, { "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University", @@ -81,9 +92,8 @@ "orcid": "0000-0003-4554-5058" }, { - "affiliation": "Developer", - "name": "Clark, Daniel", - "orcid": "0000-0002-8121-8954" + "affiliation": "National Institutes of Health", + "name": "Clark, Michael G. " }, { "affiliation": "Mayo Clinic, Neurology, Rochester, MN, USA", @@ -91,45 +101,35 @@ "orcid": "0000-0002-2666-0969" }, { - "affiliation": "MIT", - "name": "Goncalves, Mathias" - }, - { - "name": "Loney, Fred" + "affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering", + "name": "Keshavan, Anisha", + "orcid": "0000-0003-3554-043X" }, { - "affiliation": "National Institute of Mental Health", - "name": "Nielson, Dylan M.", - "orcid": "0000-0003-4613-6643" + "affiliation": "UC Berkeley", + "name": "Clark, Dav", + "orcid": "0000-0002-3982-4416" }, { - "name": "Madison, Cindee" + "name": "Pinsard, Basile" }, { "affiliation": "CNRS LTCI, Telecom ParisTech, Universit\u00e9 Paris-Saclay", "name": "Gramfort, Alexandre", "orcid": "0000-0001-9791-4404" }, - { - "affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering", - "name": "Keshavan, Anisha", - "orcid": "0000-0003-3554-043X" - }, { "name": "Berleant, Shoshana" }, { - "affiliation": "Montreal Neurological Institute and Hospital", - "name": "Markello, Ross", - "orcid": "0000-0003-1057-1336" - }, - { - "name": "Pinsard, Basile" + "affiliation": "National Institute of Mental Health", + "name": "Nielson, Dylan M.", + "orcid": "0000-0003-4613-6643" }, { - "affiliation": "UC Berkeley", - "name": "Clark, Dav", - "orcid": "0000-0002-3982-4416" + "affiliation": "INRIA", + "name": "Varoquaux, Gael", + "orcid": "0000-0003-1076-5122" }, { "affiliation": "UC San Diego", @@ -137,52 +137,57 @@ "orcid": "0000-0002-7782-0790" }, { - "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich", - "name": "Horea, Christian", - "orcid": "0000-0001-7037-2449" + "affiliation": "National Institute of Mental Health", + "name": "Nielson, Dylan M.", + "orcid": "0000-0003-4613-6643" }, { - "affiliation": "Molecular Imaging Research Center, CEA, France", - "name": "Bougacha, Salma" + "affiliation": "Montreal Neurological Institute and Hospital", + "name": "Markello, Ross", + "orcid": "0000-0003-1057-1336" }, { - "affiliation": "INRIA", - "name": "Varoquaux, Gael", - "orcid": "0000-0003-1076-5122" + "affiliation": "The University of Washington eScience Institute", + "name": "Rokem, Ariel", + "orcid": "0000-0003-0679-1985" }, { "affiliation": "Athena EPI, Inria Sophia-Antipolis", "name": "Wassermann , Demian", "orcid": "0000-0001-5194-6056" }, - { - "affiliation": "The University of Washington eScience Institute", - "name": "Rokem, Ariel", - "orcid": "0000-0003-0679-1985" - }, { "affiliation": "Dartmouth College: Hanover, NH, United States", "name": "Halchenko, Yaroslav O.", "orcid": "0000-0003-3456-2493" }, { - "name": "Moloney, Brendan" - }, - { - "affiliation": "University College London", - "name": "Malone, Ian B.", - "orcid": "0000-0001-7512-7856" + "affiliation": "Dartmouth College", + "name": "Visconti di Oleggio Castello, Matteo", + "orcid": "0000-0001-7931-5272" }, { "affiliation": "MIT", "name": "Kaczmarzyk, Jakub", "orcid": "0000-0002-5544-7577" }, + { + "name": "Moloney, Brendan" + }, { "affiliation": "Otto-von-Guericke-University Magdeburg, Germany", "name": "Hanke, Michael", "orcid": "0000-0001-6398-6370" }, + { + "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich", + "name": "Horea, Christian", + "orcid": "0000-0001-7037-2449" + }, + { + "affiliation": "Molecular Imaging Research Center, CEA, France", + "name": "Bougacha, Salma" + }, { "affiliation": "Vrije Universiteit, Amsterdam", "name": "Gilles de Hollander", @@ -195,28 +200,17 @@ "name": "Buchanan, Colin" }, { - "affiliation": "California Institute of Technology", - "name": "Pauli, Wolfgang M.", - "orcid": "0000-0002-0966-0254" - }, - { - "affiliation": "Research Group Neuroanatomy and Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany", - "name": "Huntenburg, Julia M.", - "orcid": "0000-0003-0579-9811" - }, - { - "name": "Forbes, Jessica" - }, - { - "affiliation": "Montreal Neurological Institute and Hospital", - "name": "DuPre, Elizabeth", - "orcid": "0000-0003-1358-196X" + "name": "Tungaraza, Rosalia" }, { - "name": "Schwartz, Yannick" + "affiliation": "University College London", + "name": "Mancini, Matteo", + "orcid": "0000-0001-7194-4568" }, { - "name": "Tungaraza, Rosalia" + "affiliation": "California Institute of Technology", + "name": "Pauli, Wolfgang M.", + "orcid": "0000-0002-0966-0254" }, { "affiliation": "Duke University", @@ -224,68 +218,89 @@ "orcid": "0000-0003-2766-8425" }, { - "name": "Kent, James" + "affiliation": "Nathan s Kline institute for psychiatric research", + "name": "Sikka, Sharad" }, { - "name": "Perez-Guevara, Martin" + "name": "Schwartz, Yannick" }, { - "affiliation": "UniversityHospital Heidelberg, Germany", - "name": "Kleesiek, Jens" + "affiliation": "University College London", + "name": "Malone, Ian B.", + "orcid": "0000-0001-7512-7856" }, { - "affiliation": "Nathan s Kline institute for psychiatric research", - "name": "Sikka, Sharad" + "affiliation": "Montreal Neurological Institute and Hospital", + "name": "DuPre, Elizabeth", + "orcid": "0000-0003-1358-196X" }, { - "name": "Watanabe, Aimi" + "affiliation": "Child Mind Institute", + "name": "Frohlich, Caroline" }, { "affiliation": "University of Iowa", "name": "Welch, David" }, { - "affiliation": "Child Mind Institute", - "name": "Frohlich, Caroline" + "name": "Forbes, Jessica" + }, + { + "name": "Watanabe, Aimi" }, { "name": "Cumba, Chad" }, { - "name": "Ginsburg, Daniel" + "affiliation": "Research Group Neuroanatomy and Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany", + "name": "Huntenburg, Julia M.", + "orcid": "0000-0003-0579-9811" }, { "affiliation": "University College London", "name": "Eshaghi, Arman", "orcid": "0000-0002-6652-3512" }, - { - "affiliation": "University of Texas at Austin", - "name": "De La Vega, Alejandro", - "orcid": "0000-0001-9062-3778" - }, { "affiliation": "Harvard University - Psychology", "name": "Kastman, Erik", "orcid": "0000-0001-7221-9042" }, { - "name": "Blair, Ross" + "name": "Ginsburg, Daniel" + }, + { + "affiliation": "National University Singapore", + "name": "Schaefer, Alexander", + "orcid": "0000-0001-6488-4739" }, { "affiliation": "Washington University in St Louis", "name": "Acland, Benjamin", "orcid": "0000-0001-6392-6634" }, + { + "name": "Kent, James" + }, + { + "name": "Perez-Guevara, Martin" + }, { "affiliation": "Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation; University of Queensland", "name": "Gillman, Ashley", "orcid": "0000-0001-9130-1092" }, { - "affiliation": "National University Singapore", - "name": "Schaefer, Alexander", - "orcid": "0000-0001-6488-4739" + "affiliation": "Molecular Imaging Research Center, CEA, France", + "name": "Bougacha, Salma" + }, + { + "name": "Forbes, Jessica" + }, + { + "affiliation": "Montreal Neurological Institute and Hospital", + "name": "DuPre, Elizabeth", + "orcid": "0000-0003-1358-196X" }, { "affiliation": "SRI International", @@ -296,55 +311,48 @@ "affiliation": "Child Mind Institute", "name": "Giavasis, Steven" }, - { - "name": "Correa, Carlos" - }, - { - "name": "Ghayoor, Ali" - }, { "affiliation": "University of California, San Francisco", "name": "Jordan, Kesshi", "orcid": "0000-0001-6313-0580" }, { - "name": "Erickson, Drew" + "affiliation": "UniversityHospital Heidelberg, Germany", + "name": "Kleesiek, Jens" }, { - "name": "K\u00fcttner, Ren\u00e9" + "name": "Erickson, Drew" }, { - "name": "Zhou, Dale" + "name": "K\u00fcttner, Ren\u00e9" }, { "name": "Haselgrove, Christian" }, { - "name": "Haehn, Daniel" + "name": "Correa, Carlos" }, { - "affiliation": "MPI CBS Leipzig, Germany", - "name": "Lampe, Leonie" + "name": "Ghayoor, Ali" }, { "name": "Millman, Jarrod" }, { - "affiliation": "University of California, San Francisco", - "name": "Jordan, Kesshi", - "orcid": "0000-0001-6313-0580" + "name": "Haehn, Daniel" + }, + { + "affiliation": "MPI CBS Leipzig, Germany", + "name": "Lampe, Leonie" }, { "name": "Lai, Jeff" }, { - "affiliation": "The University of Sydney", - "name": "Liu, Siqi" + "name": "Zhou, Dale" }, { - "affiliation": "Leibniz Institute for Neurobiology", - "name": "Stadler, J\u00f6rg", - "orcid": "0000-0003-4313-129X" + "name": "Blair, Ross" }, { "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.", @@ -354,49 +362,45 @@ { "name": "Renfro, Mandy" }, + { + "affiliation": "The University of Sydney", + "name": "Liu, Siqi" + }, { "affiliation": "University of Pennsylvania", "name": "Kahn, Ari E.", "orcid": "0000-0002-2127-0507" }, - { - "affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China; Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands", - "name": "Kong, Xiang-Zhen", - "orcid": "0000-0002-0805-1350" - }, { "affiliation": "Department of Psychology, Stanford University", "name": "Triplett, William", "orcid": "0000-0002-9546-1306" }, { - "name": "Park, Anne" - }, - { - "name": "Hallquist, Michael" - }, - { - "name": "McDermottroe, Conor" + "affiliation": "University of California, San Francisco", + "name": "Jordan, Kesshi", + "orcid": "0000-0001-6313-0580" }, { - "name": "Poldrack, Russell" + "affiliation": "Leibniz Institute for Neurobiology", + "name": "Stadler, J\u00f6rg", + "orcid": "0000-0003-4313-129X" }, { - "affiliation": "Boston University", - "name": "Perkins, L. Nathan" + "affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China; Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands", + "name": "Kong, Xiang-Zhen", + "orcid": "0000-0002-0805-1350" }, { - "affiliation": "University of California, San Francisco", - "name": "Jordan, Kesshi", - "orcid": "0000-0001-6313-0580" + "name": "Hallquist, Michael" }, { - "affiliation": "University of Newcastle, Australia", - "name": "Cooper, Gavin", - "orcid": "0000-0002-7186-5293" + "name": "McDermottroe, Conor" }, { - "name": "Noel, Maxime" + "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging", + "name": "Chetverikov, Andrey", + "orcid": "0000-0003-2767-6310" }, { "name": "Salvatore, John" @@ -405,12 +409,15 @@ "name": "Mertz, Fred" }, { - "name": "Inati, Souheil" + "name": "Park, Anne" }, { - "affiliation": "University of Amsterdam", - "name": "Lukas Snoek", - "orcid": "0000-0001-8972-204X" + "name": "Poldrack, Russell" + }, + { + "affiliation": "University of California, San Francisco", + "name": "Jordan, Kesshi", + "orcid": "0000-0001-6313-0580" }, { "affiliation": "Child Mind Institute", @@ -418,20 +425,19 @@ "orcid": "0000-0002-4950-1303" }, { - "name": "Hinds, Oliver" + "name": "Inati, Souheil" }, { - "affiliation": "Institute of Neuroinformatics, ETH/University of Zurich", - "name": "Gerhard, Stephan", - "orcid": "0000-0003-4454-6171" + "name": "Hinds, Oliver" }, { - "name": "Rothmei, Simon" + "affiliation": "University of Newcastle, Australia", + "name": "Cooper, Gavin", + "orcid": "0000-0002-7186-5293" }, { - "affiliation": "University of Helsinki", - "name": "Andberg, Sami Kristian", - "orcid": "0000-0002-5650-3964" + "affiliation": "Boston University", + "name": "Perkins, L. Nathan" }, { "name": "Tambini, Arielle" @@ -443,28 +449,29 @@ "name": "Mattfeld, Aaron" }, { - "name": "Urchs, Sebastian" + "name": "Noel, Maxime" }, { - "affiliation": "University of illinois urbana champaign", - "name": "Sharp, Paul" + "affiliation": "University of Amsterdam", + "name": "Lukas Snoek", + "orcid": "0000-0001-8972-204X" }, { - "name": "Brett, Matthew" + "name": "Matsubara, K" }, { - "name": "Matsubara, K" + "name": "Cheung, Brian" }, { - "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry", - "name": "Geisler, Daniel", - "orcid": "0000-0003-2076-5329" + "affiliation": "Institute of Neuroinformatics, ETH/University of Zurich", + "name": "Gerhard, Stephan", + "orcid": "0000-0003-4454-6171" }, { - "name": "Cheung, Brian" + "name": "Rothmei, Simon" }, { - "name": "Nickson, Thomas" + "name": "Urchs, Sebastian" }, { "affiliation": "Medical Imaging & Biomarkers, Bioclinica, Newark, CA, USA.", @@ -472,7 +479,14 @@ "orcid": "0000-0002-0744-5155" }, { - "name": "Weinstein, Alejandro" + "affiliation": "Department of Psychology, Stanford University; Parietal, INRIA", + "name": "Durnez, Joke", + "orcid": "0000-0001-9030-2202" + }, + { + "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry", + "name": "Geisler, Daniel", + "orcid": "0000-0003-2076-5329" }, { "affiliation": "The University of Texas at Austin", @@ -480,26 +494,29 @@ "orcid": "0000-0003-3618-2056" }, { - "affiliation": "Duke University", - "name": "Broderick, William", - "orcid": "0000-0002-8999-9003" + "affiliation": "University of illinois urbana champaign", + "name": "Sharp, Paul" }, { - "name": "Dubois, Mathieu" + "affiliation": "University College London", + "name": "Mancini, Matteo", + "orcid": "0000-0001-7194-4568" }, { - "affiliation": "Department of Psychology, Stanford University; Parietal, INRIA", - "name": "Durnez, Joke", - "orcid": "0000-0001-9030-2202" + "name": "Weinstein, Alejandro" }, { - "name": "Arias, Jaime" + "affiliation": "Duke University", + "name": "Broderick, William", + "orcid": "0000-0002-8999-9003" }, { - "name": "Tarbert, Claire" + "name": "Saase, Victor" }, { - "name": "Saase, Victor" + "affiliation": "University of Helsinki", + "name": "Andberg, Sami Kristian", + "orcid": "0000-0002-5650-3964" }, { "name": "Harms, Robbert" @@ -507,23 +524,40 @@ { "name": "Khanuja, Ranjeet" }, - { - "name": "Podranski, Kornelius" - }, { "name": "Schlamp, Kai" }, { - "name": "Flandin, Guillaume" + "name": "Arias, Jaime" }, { "affiliation": "CEA", "name": "Papadopoulos Orfanos, Dimitri", "orcid": "0000-0002-1242-8990" }, + { + "name": "Tarbert, Claire" + }, + { + "affiliation": "University of Texas at Austin", + "name": "De La Vega, Alejandro", + "orcid": "0000-0001-9062-3778" + }, + { + "name": "Nickson, Thomas" + }, + { + "name": "Brett, Matthew" + }, + { + "name": "Dubois, Mathieu" + }, { "name": "Falkiewicz, Marcel" }, + { + "name": "Podranski, Kornelius" + }, { "affiliation": "Child Mind Institute / Nathan Kline Institute", "name": "Pellman, John", @@ -540,6 +574,9 @@ { "name": "Schwabacher, Isaac" }, + { + "name": "Flandin, Guillaume" + }, { "name": "Liem, Franz" }, @@ -563,16 +600,6 @@ "affiliation": "MIT, HMS", "name": "Ghosh, Satrajit", "orcid": "0000-0002-5312-6729" - }, - { - "affiliation": "University College London", - "name": "Mancini, Matteo", - "orcid": "0000-0001-7194-4568" - }, - { - "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging", - "name": "Chetverikov, Andrey", - "orcid": "0000-0003-2767-6310" } ], "keywords": [ From 2c855f08d09160e04246cb8d101f4db4224b8bfd Mon Sep 17 00:00:00 2001 From: mathiasg Date: Mon, 22 Jan 2018 11:00:30 -0500 Subject: [PATCH 2/5] add: missing autotests --- .../afni/tests/test_auto_ConvertDset.py | 63 ++++--- .../ants/tests/test_auto_Registration.py | 166 ++++++++++++++++++ .../niftyseg/tests/test_auto_PatchMatch.py | 60 +++++++ 3 files changed, 262 insertions(+), 27 deletions(-) create mode 100644 nipype/interfaces/ants/tests/test_auto_Registration.py create mode 100644 nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py diff --git a/nipype/interfaces/afni/tests/test_auto_ConvertDset.py b/nipype/interfaces/afni/tests/test_auto_ConvertDset.py index c6e73f4ecf..03739bf972 100644 --- a/nipype/interfaces/afni/tests/test_auto_ConvertDset.py +++ b/nipype/interfaces/afni/tests/test_auto_ConvertDset.py @@ -4,40 +4,49 @@ def test_ConvertDset_inputs(): - input_map = dict(args=dict(argstr='%s', - ), - environ=dict(nohash=True, - usedefault=True, - ), - ignore_exception=dict(deprecated='1.0.0', - nohash=True, - usedefault=True, - ), - in_file=dict(argstr='-input %s', - mandatory=True, - position=-2, - ), - out_file=dict(argstr='-prefix %s', - position=-1, - ), - out_type=dict(argstr='-o_%s', - mandatory=True, - position=0, - ), - terminal_output=dict(deprecated='1.0.0', - nohash=True, - ), + input_map = dict( + args=dict(argstr='%s', ), + environ=dict( + nohash=True, + usedefault=True, + ), + ignore_exception=dict( + deprecated='1.0.0', + nohash=True, + usedefault=True, + ), + in_file=dict( + argstr='-input %s', + mandatory=True, + position=-2, + ), + num_threads=dict( + nohash=True, + usedefault=True, + ), + out_file=dict( + argstr='-prefix %s', + mandatory=True, + position=-1, + ), + out_type=dict( + argstr='-o_%s', + mandatory=True, + position=0, + ), + outputtype=dict(), + terminal_output=dict( + deprecated='1.0.0', + nohash=True, + ), ) inputs = ConvertDset.input_spec() for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value - - def test_ConvertDset_outputs(): - output_map = dict(out_file=dict(), - ) + output_map = dict(out_file=dict(), ) outputs = ConvertDset.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_Registration.py b/nipype/interfaces/ants/tests/test_auto_Registration.py new file mode 100644 index 0000000000..4d41498314 --- /dev/null +++ b/nipype/interfaces/ants/tests/test_auto_Registration.py @@ -0,0 +1,166 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from __future__ import unicode_literals +from ..registration import Registration + + +def test_Registration_inputs(): + input_map = dict( + args=dict(argstr='%s', ), + collapse_output_transforms=dict( + argstr='--collapse-output-transforms %d', + usedefault=True, + ), + convergence_threshold=dict( + requires=['number_of_iterations'], + usedefault=True, + ), + convergence_window_size=dict( + requires=['convergence_threshold'], + usedefault=True, + ), + dimension=dict( + argstr='--dimensionality %d', + usedefault=True, + ), + environ=dict( + nohash=True, + usedefault=True, + ), + fixed_image=dict(mandatory=True, ), + fixed_image_mask=dict( + argstr='%s', + max_ver='2.1.0', + xor=['fixed_image_masks'], + ), + fixed_image_masks=dict( + min_ver='2.2.0', + xor=['fixed_image_mask'], + ), + float=dict(argstr='--float %d', ), + ignore_exception=dict( + deprecated='1.0.0', + nohash=True, + usedefault=True, + ), + initial_moving_transform=dict( + argstr='%s', + xor=['initial_moving_transform_com'], + ), + initial_moving_transform_com=dict( + argstr='%s', + xor=['initial_moving_transform'], + ), + initialize_transforms_per_stage=dict( + argstr='--initialize-transforms-per-stage %d', + usedefault=True, + ), + interpolation=dict( + argstr='%s', + usedefault=True, + ), + interpolation_parameters=dict(), + invert_initial_moving_transform=dict( + requires=['initial_moving_transform'], + xor=['initial_moving_transform_com'], + ), + metric=dict(mandatory=True, ), + metric_item_trait=dict(), + metric_stage_trait=dict(), + metric_weight=dict( + mandatory=True, + requires=['metric'], + usedefault=True, + ), + metric_weight_item_trait=dict(), + metric_weight_stage_trait=dict(), + moving_image=dict(mandatory=True, ), + moving_image_mask=dict( + max_ver='2.1.0', + requires=['fixed_image_mask'], + xor=['moving_image_masks'], + ), + moving_image_masks=dict( + min_ver='2.2.0', + xor=['moving_image_mask'], + ), + num_threads=dict( + nohash=True, + usedefault=True, + ), + number_of_iterations=dict(), + output_inverse_warped_image=dict( + hash_files=False, + requires=['output_warped_image'], + ), + output_transform_prefix=dict( + argstr='%s', + usedefault=True, + ), + output_warped_image=dict(hash_files=False, ), + radius_bins_item_trait=dict(), + radius_bins_stage_trait=dict(), + radius_or_number_of_bins=dict( + requires=['metric_weight'], + usedefault=True, + ), + restore_state=dict(argstr='--restore-state %s', ), + restrict_deformation=dict(), + sampling_percentage=dict(requires=['sampling_strategy'], ), + sampling_percentage_item_trait=dict(), + sampling_percentage_stage_trait=dict(), + sampling_strategy=dict(requires=['metric_weight'], ), + sampling_strategy_item_trait=dict(), + sampling_strategy_stage_trait=dict(), + save_state=dict(argstr='--save-state %s', ), + shrink_factors=dict(mandatory=True, ), + sigma_units=dict(requires=['smoothing_sigmas'], ), + smoothing_sigmas=dict(mandatory=True, ), + terminal_output=dict( + deprecated='1.0.0', + nohash=True, + ), + transform_parameters=dict(), + transforms=dict( + argstr='%s', + mandatory=True, + ), + use_estimate_learning_rate_once=dict(), + use_histogram_matching=dict(usedefault=True, ), + verbose=dict(argstr='-v', ), + winsorize_lower_quantile=dict( + argstr='%s', + usedefault=True, + ), + winsorize_upper_quantile=dict( + argstr='%s', + usedefault=True, + ), + write_composite_transform=dict( + argstr='--write-composite-transform %d', + usedefault=True, + ), + ) + inputs = Registration.input_spec() + + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(inputs.traits()[key], metakey) == value +def test_Registration_outputs(): + output_map = dict( + composite_transform=dict(), + elapsed_time=dict(), + forward_invert_flags=dict(), + forward_transforms=dict(), + inverse_composite_transform=dict(), + inverse_warped_image=dict(), + metric_value=dict(), + reverse_invert_flags=dict(), + reverse_transforms=dict(), + save_state=dict(), + warped_image=dict(), + ) + outputs = Registration.output_spec() + + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py b/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py new file mode 100644 index 0000000000..718eba4e78 --- /dev/null +++ b/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py @@ -0,0 +1,60 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from __future__ import unicode_literals +from ..patchmatch import PatchMatch + + +def test_PatchMatch_inputs(): + input_map = dict( + args=dict(argstr='%s', ), + cs_size=dict(argstr='-cs %i', ), + database_file=dict( + argstr='-db %s', + mandatory=True, + position=3, + ), + environ=dict( + nohash=True, + usedefault=True, + ), + ignore_exception=dict( + deprecated='1.0.0', + nohash=True, + usedefault=True, + ), + in_file=dict( + argstr='-i %s', + mandatory=True, + position=1, + ), + it_num=dict(argstr='-it %i', ), + mask_file=dict( + argstr='-m %s', + mandatory=True, + position=2, + ), + match_num=dict(argstr='-match %i', ), + out_file=dict( + argstr='-o %s', + name_source=['in_file'], + name_template='%s_pm.nii.gz', + position=4, + ), + patch_size=dict(argstr='-size %i', ), + pm_num=dict(argstr='-pm %i', ), + terminal_output=dict( + deprecated='1.0.0', + nohash=True, + ), + ) + inputs = PatchMatch.input_spec() + + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(inputs.traits()[key], metakey) == value +def test_PatchMatch_outputs(): + output_map = dict(out_file=dict(), ) + outputs = PatchMatch.output_spec() + + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(outputs.traits()[key], metakey) == value From d9c7c27bfc7592a6f4b82af420a584235af2b3d4 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Mon, 22 Jan 2018 11:02:30 -0500 Subject: [PATCH 3/5] maint: add yapf to dependencies --- nipype/info.py | 1 + requirements.txt | 1 + 2 files changed, 2 insertions(+) diff --git a/nipype/info.py b/nipype/info.py index 884926f46d..55f1e5a084 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -148,6 +148,7 @@ def get_nipype_gitversion(): 'pydotplus', 'pydot>=%s' % PYDOT_MIN_VERSION, 'packaging', + 'yapf' ] if sys.version_info <= (3, 4): diff --git a/requirements.txt b/requirements.txt index a5ac0a5683..806ff244f0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,3 +15,4 @@ mock pydotplus pydot>=1.2.3 packaging +yapf From efb045bb3c042af3959ef7adb361d29bcde4b0d8 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Mon, 22 Jan 2018 11:22:26 -0500 Subject: [PATCH 4/5] maint: update mailmap + fix spacing in docs --- .mailmap | 3 +++ doc/quickstart.rst | 1 + 2 files changed, 4 insertions(+) diff --git a/.mailmap b/.mailmap index 0a982fb8a9..59d6d745a2 100644 --- a/.mailmap +++ b/.mailmap @@ -14,6 +14,7 @@ Ariel Rokem arokem Arman Eshaghi armaneshaghi Ashely Gillman Ashley Gillman Ashely Gillman ashgillman +Andrey Chetverikov achetverikov Basille Pinsard bpinsard Basille Pinsard bpinsard Ben Cipollini Ben Cipollini @@ -79,6 +80,8 @@ Kevin Sitek sitek Leonie Lampe Leonie Lmape Lukas Snoek Lukas Snoek Mathias Goncalves mathiasg +Matteo Mancini matteomancini +Matteo Visconti dOC mvdoc Michael Dayan Michael Michael Dayan Michael Michael Dayan mick-d diff --git a/doc/quickstart.rst b/doc/quickstart.rst index 81fed9f5e6..ee856d5fb2 100644 --- a/doc/quickstart.rst +++ b/doc/quickstart.rst @@ -47,6 +47,7 @@ Learning Resources ================== `Porcupine `_ : create Nipype pipelines using a graphical interface + View the `examples gallery here `_ Developer guides From 18417415a597dabbb594820ef086a2ca357aa7fa Mon Sep 17 00:00:00 2001 From: mathiasg Date: Mon, 22 Jan 2018 17:04:05 -0500 Subject: [PATCH 5/5] fix: remove yapf from runtime reqs --- nipype/info.py | 1 - requirements.txt | 1 - 2 files changed, 2 deletions(-) diff --git a/nipype/info.py b/nipype/info.py index 55f1e5a084..884926f46d 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -148,7 +148,6 @@ def get_nipype_gitversion(): 'pydotplus', 'pydot>=%s' % PYDOT_MIN_VERSION, 'packaging', - 'yapf' ] if sys.version_info <= (3, 4): diff --git a/requirements.txt b/requirements.txt index 806ff244f0..a5ac0a5683 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,4 +15,3 @@ mock pydotplus pydot>=1.2.3 packaging -yapf