diff --git a/.mailmap b/.mailmap index f7d32274fb..0a982fb8a9 100644 --- a/.mailmap +++ b/.mailmap @@ -1,5 +1,6 @@ Aimi Watanabe stymy Aimi Watanabe stymy +Alejandro de la Vega adelavega Alexander Schaefer Alexander Schaefer Alexander Schaefer alexschaefer83 Alexander Schaefer aschaefer @@ -56,11 +57,13 @@ Franz Liem fliem Gael Varoquaux GaelVaroquaux Gael Varoquaux GaelVaroquaux Gavin Cooper gjcooper +Gilles de Hollander Gilles86 Hans Johnson Hans Johnson Hans Johnson hjmjohnson Horea Christian Horea Christian Isaac Schwabacher ischwabacher James Kent jdkent +Jakub Kaczmarzyk kaczmarj Jason Wong Jason Jason Wong jason Jason Wong Jason W @@ -72,7 +75,9 @@ Joerg Stadler Jörg Stadler jokedurnez Josh Warner Josh Warner (Mac) Kai Schlamp medihack Jessica Forbes jessicaforbes +Kevin Sitek sitek Leonie Lampe Leonie Lmape +Lukas Snoek Lukas Snoek Mathias Goncalves mathiasg Michael Dayan Michael Michael Dayan Michael @@ -102,5 +107,6 @@ Steven Giavasis sgiavasis Tristan Glatard Tristan Glatard Victor Saase vsaase William Triplett William Triplett +Wolfgang Pauli Wolfgang Pauli Yaroslav Halchenko Yaroslav Halchenko pipolose pipolose diff --git a/.travis.yml b/.travis.yml index 681d3dd765..08d9234675 100644 --- a/.travis.yml +++ b/.travis.yml @@ -59,4 +59,4 @@ deploy: tags: true repo: nipy/nipype branch: master - distributions: "sdist" + distributions: "sdist bdist_wheel" diff --git a/.zenodo.json b/.zenodo.json index 41497da6d8..2985b7e107 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -514,11 +514,6 @@ { "name": "Shachnev, Dmitry" }, - { - "affiliation": "MIT, HMS", - "name": "Ghosh, Satrajit", - "orcid": "0000-0002-5312-6729" - }, { "affiliation": "University of Amsterdam", "name": "Lukas Snoek", @@ -538,6 +533,11 @@ "affiliation": "MIT", "name": "Kaczmarzyk, Jakub", "orcid": "0000-0002-5544-7577" + }, + { + "affiliation": "MIT, HMS", + "name": "Ghosh, Satrajit", + "orcid": "0000-0002-5312-6729" } ], "keywords": [ diff --git a/CHANGES b/CHANGES index f7761f7b91..c4ff9ea953 100644 --- a/CHANGES +++ b/CHANGES @@ -1,6 +1,14 @@ -Upcoming release (0.14.0) +Upcoming release ================ +0.14.0 (November 21, 2017) +========================== + +###### [Full changelog](https://github.com/nipy/nipype/milestone/13) + +* ENH: Generate Dockerfiles with neurodocker (https://github.com/nipy/nipype/pull/2202) +* ENH: FLAIR options for recon-all (https://github.com/nipy/nipype/pull/2279) +* ENH: Config option for setting maxtasksperchild when multiprocessing (https://github.com/nipy/nipype/pull/2284) * FIX: Testing maintainance and improvements (https://github.com/nipy/nipype/pull/2252) * ENH: Add elapsed_time and final metric_value to ants.Registration (https://github.com/nipy/nipype/pull/1985) * ENH: Improve terminal_output feature (https://github.com/nipy/nipype/pull/2209) @@ -17,7 +25,7 @@ Upcoming release (0.14.0) * MAINT: Additional Windows support (https://github.com/nipy/nipype/pull/2085) * ENH: Output realignment matrices from TOPUP (https://github.com/nipy/nipype/pull/2084) * ENH: Additional AFNI interfaces: 3dZcat, 3dZeropad, 3dedge3, 3dDeconvolve, 3dQwarp, 1dCat, 3dNwarpApply, 3daxialize, - 3dREMLfit, 3dUndump, 3dCM, 3dSynthesize + more (https://github.com/nipy/nipype/pull/2087, https://github.com/nipy/nipype/pull/2090, + 3dREMLfit, 3dUndump, 3dCM, 3dSynthesize + more (https://github.com/nipy/nipype/pull/2087, https://github.com/nipy/nipype/pull/2090, https://github.com/nipy/nipype/pull/2095, https://github.com/nipy/nipype/pull/2099, https://github.com/nipy/nipype/pull/2103, https://github.com/nipy/nipype/pull/2114, https://github.com/nipy/nipype/pull/2135, https://github.com/nipy/nipype/pull/2186, https://github.com/nipy/nipype/pull/2201, https://github.com/nipy/nipype/pull/2210) diff --git a/doc/conf.py b/doc/conf.py index 65ee4c1e6a..17ba33cbee 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 = "0.13.1" +release = "0.14.0-rc1" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/doc/users/config_file.rst b/doc/users/config_file.rst index b196047e97..7c10a381c8 100644 --- a/doc/users/config_file.rst +++ b/doc/users/config_file.rst @@ -74,11 +74,11 @@ Execution *display_variable* Override the ``$DISPLAY`` environment variable for interfaces that require - an X server. This option is useful if there is a running X server, but - ``$DISPLAY`` was not defined in nipype's environment. For example, if an X + an X server. This option is useful if there is a running X server, but + ``$DISPLAY`` was not defined in nipype's environment. For example, if an X server is listening on the default port of 6000, set ``display_variable = :0`` - to enable nipype interfaces to use it. It may also point to displays provided - by VNC, `xnest `_ + to enable nipype interfaces to use it. It may also point to displays provided + by VNC, `xnest `_ or `Xvfb `_. If neither ``display_variable`` nor the ``$DISPLAY`` environment variable are set, nipype will try to configure a new virtual server using Xvfb. diff --git a/nipype/algorithms/tests/test_mesh_ops.py b/nipype/algorithms/tests/test_mesh_ops.py index 9d510dee2b..d5fbc56825 100644 --- a/nipype/algorithms/tests/test_mesh_ops.py +++ b/nipype/algorithms/tests/test_mesh_ops.py @@ -15,7 +15,7 @@ @pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed") def test_ident_distances(tmpdir): - tmpdir.chdir() + tmpdir.chdir() in_surf = example_data('surf01.vtk') dist_ident = m.ComputeMeshWarp() diff --git a/nipype/info.py b/nipype/info.py index d7b1b106d1..fad9912012 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -10,7 +10,7 @@ # full release. '.dev' as a version_extra string means this is a development # version # Remove -dev for release -__version__ = '1.0.0-dev' +__version__ = '0.14.0-rc1' def get_nipype_gitversion(): diff --git a/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py b/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py new file mode 100644 index 0000000000..da3b0fb383 --- /dev/null +++ b/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py @@ -0,0 +1,48 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from __future__ import unicode_literals +from ..utils import TCatSubBrick + + +def test_TCatSubBrick_inputs(): + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_files=dict(argstr='%s%s ...', + copyfile=False, + mandatory=True, + position=-1, + ), + num_threads=dict(nohash=True, + usedefault=True, + ), + out_file=dict(argstr='-prefix %s', + genfile=True, + ), + outputtype=dict(), + rlt=dict(argstr='-rlt%s', + position=1, + ), + terminal_output=dict(deprecated='1.0.0', + nohash=True, + ), + ) + inputs = TCatSubBrick.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_TCatSubBrick_outputs(): + output_map = dict(out_file=dict(), + ) + outputs = TCatSubBrick.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/ants/tests/test_resampling.py b/nipype/interfaces/ants/tests/test_resampling.py index 22dc4446e9..509ebfe844 100644 --- a/nipype/interfaces/ants/tests/test_resampling.py +++ b/nipype/interfaces/ants/tests/test_resampling.py @@ -1,5 +1,5 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- -# vi: set ft=python sts=4 ts=4 sw=4 et: +# vi: set ft=python sts=4 ts=4 sw=4 et: from nipype.interfaces.ants import WarpImageMultiTransform, WarpTimeSeriesImageMultiTransform import os @@ -66,7 +66,7 @@ def create_wtsimt(): def test_WarpTimeSeriesImageMultiTransform(change_dir, create_wtsimt): wtsimt = create_wtsimt assert wtsimt.cmdline == 'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii \ --R ants_deformed.nii.gz ants_Warp.nii.gz ants_Affine.txt' +-R ants_deformed.nii.gz ants_Warp.nii.gz ants_Affine.txt' def test_WarpTimeSeriesImageMultiTransform_invaffine(change_dir, create_wtsimt): diff --git a/nipype/interfaces/cmtk/tests/test_nbs.py b/nipype/interfaces/cmtk/tests/test_nbs.py index 0516390b02..03a7aa8619 100644 --- a/nipype/interfaces/cmtk/tests/test_nbs.py +++ b/nipype/interfaces/cmtk/tests/test_nbs.py @@ -31,12 +31,12 @@ def test_importerror(creating_graphs, tmpdir): graphlist = creating_graphs group1 = graphlist[:3] group2 = graphlist[3:] - + nbs = NetworkBasedStatistic() nbs.inputs.in_group1 = group1 nbs.inputs.in_group2 = group2 nbs.inputs.edge_key = "weight" - + with pytest.raises(ImportError) as e: nbs.run() assert "cviewer library is not available" == str(e.value) diff --git a/nipype/interfaces/niftyfit/asl.py b/nipype/interfaces/niftyfit/asl.py index 366f9a6eca..8f95a48192 100644 --- a/nipype/interfaces/niftyfit/asl.py +++ b/nipype/interfaces/niftyfit/asl.py @@ -147,7 +147,7 @@ class FitAsl(NiftyFitCommand): >>> from nipype.interfaces import niftyfit >>> node = niftyfit.FitAsl() >>> node.inputs.source_file = 'asl.nii.gz' - >>> node.cmdline + >>> node.cmdline 'fit_asl -source asl.nii.gz -cbf asl_cbf.nii.gz -error asl_error.nii.gz \ -syn asl_syn.nii.gz' diff --git a/nipype/interfaces/tests/test_auto_SimpleInterface.py b/nipype/interfaces/tests/test_auto_SimpleInterface.py new file mode 100644 index 0000000000..b00d1f9a3c --- /dev/null +++ b/nipype/interfaces/tests/test_auto_SimpleInterface.py @@ -0,0 +1,16 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from __future__ import unicode_literals +from ..base import SimpleInterface + + +def test_SimpleInterface_inputs(): + input_map = dict(ignore_exception=dict(nohash=True, + usedefault=True, + ), + ) + inputs = SimpleInterface.input_spec() + + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(inputs.traits()[key], metakey) == value + diff --git a/nipype/pipeline/engine/tests/test_utils.py b/nipype/pipeline/engine/tests/test_utils.py index 34ec45cfa8..23c7a16fc6 100644 --- a/nipype/pipeline/engine/tests/test_utils.py +++ b/nipype/pipeline/engine/tests/test_utils.py @@ -23,7 +23,7 @@ def test_identitynode_removal(tmpdir): def test_function(arg1, arg2, arg3): import numpy as np return (np.array(arg1) + arg2 + arg3).tolist() - + wf = pe.Workflow(name="testidentity", base_dir=tmpdir.strpath) diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000000..3c6e79cf31 --- /dev/null +++ b/setup.cfg @@ -0,0 +1,2 @@ +[bdist_wheel] +universal=1