From 0cd8e92d6bee9ed9840b8e1f994b1b401a6737e4 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Fri, 26 Oct 2018 09:41:27 -0400 Subject: [PATCH 1/7] TEST: make specs --- .../interfaces/afni/tests/test_auto_TShift.py | 1 + .../ants/tests/test_auto_AntsJointFusion.py | 4 +- nipype/interfaces/dipy/tests/test_auto_DTI.py | 1 + .../interfaces/fsl/tests/test_auto_DTIFit.py | 2 +- .../spm/tests/test_auto_RealignUnwarp.py | 85 +++++++++++++++++++ 5 files changed, 90 insertions(+), 3 deletions(-) create mode 100644 nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py diff --git a/nipype/interfaces/afni/tests/test_auto_TShift.py b/nipype/interfaces/afni/tests/test_auto_TShift.py index a1208753d9..b267986952 100644 --- a/nipype/interfaces/afni/tests/test_auto_TShift.py +++ b/nipype/interfaces/afni/tests/test_auto_TShift.py @@ -30,6 +30,7 @@ def test_TShift_inputs(): outputtype=dict(), rlt=dict(argstr='-rlt', ), rltplus=dict(argstr='-rlt+', ), + slice_encoding_direction=dict(usedefault=True, ), slice_timing=dict( argstr='-tpattern @%s', xor=['tpattern'], diff --git a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py index 292e6b398b..341f250a2c 100644 --- a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py @@ -52,8 +52,8 @@ def test_AntsJointFusion_inputs(): hash_files=False, ), out_label_post_prob_name_format=dict( - requires=['out_label_fusion', 'out_intensity_fusion_name_format'], - ), + requires=['out_label_fusion', + 'out_intensity_fusion_name_format'], ), patch_metric=dict(argstr='-m %s', ), patch_radius=dict( argstr='-p %s', diff --git a/nipype/interfaces/dipy/tests/test_auto_DTI.py b/nipype/interfaces/dipy/tests/test_auto_DTI.py index 68c9ae1437..f543856065 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DTI.py +++ b/nipype/interfaces/dipy/tests/test_auto_DTI.py @@ -20,6 +20,7 @@ def test_DTI_inputs(): def test_DTI_outputs(): output_map = dict( ad_file=dict(), + color_fa_file=dict(), fa_file=dict(), md_file=dict(), out_file=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py index af6a0ea112..b1d3b4822d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py @@ -65,8 +65,8 @@ def test_DTIFit_outputs(): V1=dict(), V2=dict(), V3=dict(), - tensor=dict(), sse=dict(), + tensor=dict(), ) outputs = DTIFit.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py new file mode 100644 index 0000000000..50b56b81e1 --- /dev/null +++ b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py @@ -0,0 +1,85 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from __future__ import unicode_literals +from ..preprocess import RealignUnwarp + + +def test_RealignUnwarp_inputs(): + input_map = dict( + est_basis_func=dict(field='uweoptions.basfcn', ), + est_first_order_effects=dict(field='uweoptions.fot', ), + est_jacobian_deformations=dict(field='uweoptions.jm', ), + est_num_of_interations=dict( + field='uweoptions.noi', + maxlen=1, + minlen=1, + usedfault=True, + ), + est_re_est_mov_par=dict(field='uweoptions.rem', ), + est_reg_factor=dict( + field='uweoptions.lambda', + maxlen=1, + minlen=1, + usedefault=True, + ), + est_reg_order=dict(field='uweoptions.regorder', ), + est_second_order_effects=dict(field='uweoptions.sot', ), + est_taylor_expansion_point=dict( + field='uweoptions.expround', + usedefault=True, + ), + est_unwarp_fwhm=dict(field='uweoptions.uwfwhm', ), + fwhm=dict(field='eoptions.fwhm', ), + in_files=dict( + copyfile=True, + field='data.scans', + mandatory=True, + ), + interp=dict(field='eoptions.einterp', ), + matlab_cmd=dict(), + mfile=dict(usedefault=True, ), + out_prefix=dict( + field='uwroptions.prefix', + usedefault=True, + ), + paths=dict(), + phase_map=dict( + copyfile=False, + field='data.pmscan', + ), + quality=dict(field='eoptions.quality', ), + register_to_mean=dict(field='eoptions.rtm', ), + reslice_interp=dict(field='uwroptions.rinterp', ), + reslice_mask=dict(field='uwroptions.mask', ), + reslice_which=dict( + field='uwroptions.uwwhich', + maxlen=2, + minlen=2, + usedefault=True, + ), + reslice_wrap=dict(field='uwroptions.wrap', ), + separation=dict(field='eoptions.sep', ), + use_mcr=dict(), + use_v8struct=dict( + min_ver='8', + usedefault=True, + ), + weight_img=dict(field='eoptions.weight', ), + wrap=dict(field='eoptions.ewrap', ), + ) + inputs = RealignUnwarp.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_RealignUnwarp_outputs(): + output_map = dict( + mean_image=dict(), + modified_in_files=dict(), + realigned_unwarped_files=dict(), + realignment_parameters=dict(), + ) + outputs = RealignUnwarp.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 5a2b056e4e2f3123eed77f2cab474289682d82e8 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Fri, 26 Oct 2018 09:42:09 -0400 Subject: [PATCH 2/7] MNT: Drop -dev from version --- nipype/info.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/info.py b/nipype/info.py index 936c6b63ee..7fff1bf068 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__ = '1.1.4-dev' +__version__ = '1.1.4' def get_nipype_gitversion(): From 25a36e46ff742b27f11fd6bacfa9522bf8507370 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Fri, 26 Oct 2018 09:51:14 -0400 Subject: [PATCH 3/7] DOC: Update changelog --- doc/changelog/1.X.X-changelog | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index f1d63af29b..0ec279e355 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -1,3 +1,27 @@ +1.1.4 (October 29, 2018) +======================== + +##### [Full changelog](https://github.com/nipy/nipype/milestone/25?closed=1) + + * FIX: Python 2.7-3.7.1 compatible NonDaemonPool (https://github.com/nipy/nipype/pull/2754) + * FIX: VRML typo (VMRL) in MeshFix (https://github.com/nipy/nipype/pull/2757) + * FIX: Refine FSL.split output identification (https://github.com/nipy/nipype/pull/2746) + * FIX: Reuse _gen_filename logic in ants.LaplacianThickness (https://github.com/nipy/nipype/pull/2734) + * FIX: Remove 'reg_term' default from dwi2tensor interface (https://github.com/nipy/nipype/pull/2731) + * FIX: Keep profile files when ``remove_unnecessary_outputs = true`` (https://github.com/nipy/nipype/pull/2718) + * ENH: Add slice_encoding_direction input to TShift (https://github.com/nipy/nipype/pull/2753) + * ENH: Add 'sse' output to FSL DTIFit interface (https://github.com/nipy/nipype/pull/2749) + * ENH: Update ``ants.LaplacianThickness`` to use ``name_source`` (https://github.com/nipy/nipype/pull/2747) + * ENH: Add tab completion for node and interface inputs properties (https://github.com/nipy/nipype/pull/2735) + * ENH: enable/disable resource monitor in the fixture per test (https://github.com/nipy/nipype/pull/2725) + * TEST: Update expected dotfile text for networkx 1.x (https://github.com/nipy/nipype/pull/2730) + * DOC: Use consistent name in reconall workflow docstring (https://github.com/nipy/nipype/pull/2758) + * MAINT: Fix prov and rdflib in nipype (https://github.com/nipy/nipype/pull/2701) + * MAINT: Correct readthedocs build error (https://github.com/nipy/nipype/pull/2723) + * MAINT: Pin codecov to <5.0 so Travis is fixed (https://github.com/nipy/nipype/pull/2728) + * CI: Lock travis pybids 0.6.5 (https://github.com/nipy/nipype/pull/2720) + + 1.1.3 (September 24, 2018) ========================== From e1ac694ee9db729c743584bd982b662c4de2a3c7 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Fri, 26 Oct 2018 09:59:16 -0400 Subject: [PATCH 4/7] DOC: Update version in docs --- doc/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index 5f8e13e278..c88feb1892 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 = "1.1.3" +release = "1.1.4" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. From 0bae9a57e6dfc9f1d00b0ffeebbc3411e9a1f2f5 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Fri, 26 Oct 2018 10:01:47 -0400 Subject: [PATCH 5/7] MNT: Update .zenodo ordering --- .zenodo.json | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 9424961ab8..2fc777db58 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -297,8 +297,9 @@ "orcid": "0000-0001-6392-6634" }, { - "affiliation": "Child Mind Institute", - "name": "Giavasis, Steven" + "affiliation": "University of Zurich", + "name": "Liem, Franz", + "orcid": "0000-0003-0646-4810" }, { "affiliation": "UniversityHospital Heidelberg, Germany", @@ -310,6 +311,10 @@ { "name": "K\u00fcttner, Ren\u00e9" }, + { + "affiliation": "Child Mind Institute", + "name": "Giavasis, Steven" + }, { "name": "Haselgrove, Christian" }, @@ -319,11 +324,6 @@ { "name": "Ghayoor, Ali" }, - { - "affiliation": "University of Zurich", - "name": "Liem, Franz", - "orcid": "0000-0003-0646-4810" - }, { "name": "Millman, Jarrod" }, @@ -385,10 +385,6 @@ "name": "Chetverikov, Andrey", "orcid": "0000-0003-2767-6310" }, - { - "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany", - "name": "Weninger, Leon" - }, { "name": "Salvatore, John" }, @@ -414,6 +410,10 @@ "name": "Cooper, Gavin", "orcid": "0000-0002-7186-5293" }, + { + "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany", + "name": "Weninger, Leon" + }, { "affiliation": "Boston University", "name": "Perkins, L. Nathan" @@ -465,6 +465,11 @@ "name": "Geisler, Daniel", "orcid": "0000-0003-2076-5329" }, + { + "affiliation": "University of Texas at Austin", + "name": "De La Vega, Alejandro", + "orcid": "0000-0001-9062-3778" + }, { "affiliation": "University of illinois urbana champaign", "name": "Sharp, Paul" @@ -518,11 +523,6 @@ { "name": "Tarbert, Claire" }, - { - "affiliation": "University of Texas at Austin", - "name": "De La Vega, Alejandro", - "orcid": "0000-0001-9062-3778" - }, { "affiliation": "Vrije Universiteit Amsterdam", "name": "Ort, Eduard" From cbeba8c071fa7f85ce26f463d35a8227db11104d Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 31 Oct 2018 12:10:22 -0400 Subject: [PATCH 6/7] DOC: Update changelog --- doc/changelog/1.X.X-changelog | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index 0ec279e355..a085d5e642 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -1,4 +1,4 @@ -1.1.4 (October 29, 2018) +1.1.4 (October 31, 2018) ======================== ##### [Full changelog](https://github.com/nipy/nipype/milestone/25?closed=1) @@ -9,13 +9,17 @@ * FIX: Reuse _gen_filename logic in ants.LaplacianThickness (https://github.com/nipy/nipype/pull/2734) * FIX: Remove 'reg_term' default from dwi2tensor interface (https://github.com/nipy/nipype/pull/2731) * FIX: Keep profile files when ``remove_unnecessary_outputs = true`` (https://github.com/nipy/nipype/pull/2718) + * ENH: Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs (https://github.com/nipy/nipype/pull/2740) + * ENH: Add compression option for bru2nii (https://github.com/nipy/nipype/pull/2762) * ENH: Add slice_encoding_direction input to TShift (https://github.com/nipy/nipype/pull/2753) * ENH: Add 'sse' output to FSL DTIFit interface (https://github.com/nipy/nipype/pull/2749) * ENH: Update ``ants.LaplacianThickness`` to use ``name_source`` (https://github.com/nipy/nipype/pull/2747) * ENH: Add tab completion for node and interface inputs properties (https://github.com/nipy/nipype/pull/2735) * ENH: enable/disable resource monitor in the fixture per test (https://github.com/nipy/nipype/pull/2725) * TEST: Update expected dotfile text for networkx 1.x (https://github.com/nipy/nipype/pull/2730) + * DOC: Move user docs from nipype to nipype_tutorial (https://github.com/nipy/nipype/pull/2726) * DOC: Use consistent name in reconall workflow docstring (https://github.com/nipy/nipype/pull/2758) + * MAINT: Use neurodocker 0.4.1 + apt install afni (https://github.com/nipy/nipype/pull/2707) * MAINT: Fix prov and rdflib in nipype (https://github.com/nipy/nipype/pull/2701) * MAINT: Correct readthedocs build error (https://github.com/nipy/nipype/pull/2723) * MAINT: Pin codecov to <5.0 so Travis is fixed (https://github.com/nipy/nipype/pull/2728) From 9daa092eaada3609d243e5ad284dc51b34e7ad36 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 31 Oct 2018 12:15:30 -0400 Subject: [PATCH 7/7] MNT: Update .zenodo ordering --- .zenodo.json | 70 ++++++++++++++++++++++++++-------------------------- 1 file changed, 35 insertions(+), 35 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 2fc777db58..1a7ba46327 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -74,20 +74,20 @@ "affiliation": "Department of Psychology, Stanford University", "name": "Waskom, Michael" }, - { - "affiliation": "Developer", - "name": "Clark, Daniel", - "orcid": "0000-0002-8121-8954" - }, { "affiliation": "Shattuck Lab, UCLA Brain Mapping Center", "name": "Wong, Jason" }, + { + "name": "Modat, Marc" + }, { "name": "Loney, Fred" }, { - "name": "Modat, Marc" + "affiliation": "Developer", + "name": "Clark, Daniel", + "orcid": "0000-0002-8121-8954" }, { "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University", @@ -141,16 +141,6 @@ { "name": "Berleant, Shoshana" }, - { - "affiliation": "MIT", - "name": "Kaczmarzyk, Jakub", - "orcid": "0000-0002-5544-7577" - }, - { - "affiliation": "INRIA", - "name": "Varoquaux, Gael", - "orcid": "0000-0003-1076-5122" - }, { "affiliation": "UC San Diego", "name": "Cipollini, Ben", @@ -176,9 +166,24 @@ "name": "DuPre, Elizabeth", "orcid": "0000-0003-1358-196X" }, + { + "affiliation": "MIT", + "name": "Kaczmarzyk, Jakub", + "orcid": "0000-0002-5544-7577" + }, { "name": "Moloney, Brendan" }, + { + "affiliation": "INRIA", + "name": "Varoquaux, Gael", + "orcid": "0000-0003-1076-5122" + }, + { + "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich", + "name": "Horea, Christian", + "orcid": "0000-0001-7037-2449" + }, { "affiliation": "Athena EPI, Inria Sophia-Antipolis", "name": "Wassermann , Demian", @@ -189,11 +194,6 @@ "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": "Vrije Universiteit, Amsterdam", "name": "Gilles de Hollander", @@ -268,11 +268,6 @@ { "name": "Cumba, Chad" }, - { - "affiliation": "Harvard University - Psychology", - "name": "Kastman, Erik", - "orcid": "0000-0001-7221-9042" - }, { "affiliation": "SRI International", "name": "Nichols, B. Nolan", @@ -283,6 +278,11 @@ "name": "Eshaghi, Arman", "orcid": "0000-0002-6652-3512" }, + { + "affiliation": "Harvard University - Psychology", + "name": "Kastman, Erik", + "orcid": "0000-0001-7221-9042" + }, { "name": "Ginsburg, Daniel" }, @@ -308,9 +308,6 @@ { "name": "Erickson, Drew" }, - { - "name": "K\u00fcttner, Ren\u00e9" - }, { "affiliation": "Child Mind Institute", "name": "Giavasis, Steven" @@ -324,6 +321,9 @@ { "name": "Ghayoor, Ali" }, + { + "name": "K\u00fcttner, Ren\u00e9" + }, { "name": "Millman, Jarrod" }, @@ -399,9 +399,6 @@ "name": "Craddock, R. Cameron", "orcid": "0000-0002-4950-1303" }, - { - "name": "Inati, Souheil" - }, { "name": "Hinds, Oliver" }, @@ -414,6 +411,9 @@ "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany", "name": "Weninger, Leon" }, + { + "name": "Inati, Souheil" + }, { "affiliation": "Boston University", "name": "Perkins, L. Nathan" @@ -443,9 +443,6 @@ "name": "Floren, Andrew", "orcid": "0000-0003-3618-2056" }, - { - "name": "Rothmei, Simon" - }, { "name": "Urchs, Sebastian" }, @@ -498,6 +495,9 @@ { "name": "Saase, Victor" }, + { + "name": "Rothmei, Simon" + }, { "affiliation": "University of Helsinki", "name": "Andberg, Sami Kristian",