diff --git a/.zenodo.json b/.zenodo.json index 007a43c415..9fccdcc316 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -89,16 +89,16 @@ "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" }, @@ -106,15 +106,15 @@ "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" }, diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index adf20cf8e9..5dfb3f3cb7 100644 --- a/doc/changelog/1.X.X-changelog +++ b/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) diff --git a/doc/conf.py b/doc/conf.py index ec9e84f487..b8c8e5ac3e 100644 --- a/doc/conf.py +++ b/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. diff --git a/nipype/info.py b/nipype/info.py index be6edb713f..b2b87c2295 100644 --- a/nipype/info.py +++ b/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(): diff --git a/nipype/interfaces/fsl/tests/test_auto_Eddy.py b/nipype/interfaces/fsl/tests/test_auto_Eddy.py index c3cebf6937..55d9409e17 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Eddy.py +++ b/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()