From 7485570b7805fa00e2f4465057c012a22e89408a Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 26 Nov 2018 09:09:08 -0500 Subject: [PATCH 01/10] DOC: 1.1.6 Changelog --- doc/changelog/1.X.X-changelog | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index 1914257bf6..6882da62db 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -1,3 +1,20 @@ +1.1.6 (November 26, 2018) +========================= + + * [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) + * [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) ========================= From abd805d82b9f03a0b5f0c1b32a7918ba29a3da0b Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 26 Nov 2018 09:09:28 -0500 Subject: [PATCH 02/10] MNT: Version 1.1.6 --- nipype/info.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/info.py b/nipype/info.py index 9e162524dd..ff0a36e62c 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__ = '1.1.6-dev' +__version__ = '1.1.6' def get_nipype_gitversion(): From 0d0b05f90bac1568a07ce6744a3b2ab149317e6f Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 26 Nov 2018 09:20:29 -0500 Subject: [PATCH 03/10] TEST: make specs --- nipype/interfaces/tests/test_auto_MeshFix.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/nipype/interfaces/tests/test_auto_MeshFix.py b/nipype/interfaces/tests/test_auto_MeshFix.py index 48c689d2ea..f306f4abed 100644 --- a/nipype/interfaces/tests/test_auto_MeshFix.py +++ b/nipype/interfaces/tests/test_auto_MeshFix.py @@ -20,19 +20,23 @@ def test_MeshFix_inputs(): epsilon_angle=dict(argstr='-a %f', ), finetuning_distance=dict( argstr='%f', + position=-2, requires=['finetuning_substeps'], ), finetuning_inwards=dict( argstr='--fineTuneIn ', + position=-3, requires=['finetuning_distance', 'finetuning_substeps'], ), finetuning_outwards=dict( argstr='--fineTuneOut ', + position=-3, requires=['finetuning_distance', 'finetuning_substeps'], xor=['finetuning_inwards'], ), finetuning_substeps=dict( argstr='%d', + position=-1, requires=['finetuning_distance'], ), in_file1=dict( @@ -89,8 +93,6 @@ def test_MeshFix_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value - - def test_MeshFix_outputs(): output_map = dict(mesh_file=dict(), ) outputs = MeshFix.output_spec() From 9f30f79e739379969c7b71357cdecd30e25af138 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 26 Nov 2018 09:21:23 -0500 Subject: [PATCH 04/10] MAINT: Update zenodo ordering --- .zenodo.json | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 2c92959ecb..010329efb6 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -380,6 +380,11 @@ { "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", @@ -454,9 +459,6 @@ { "name": "Mertz, Fred" }, - { - "name": "Haehn, Daniel" - }, { "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry", "name": "Geisler, Daniel", @@ -481,6 +483,9 @@ "name": "Molina-Romero, Miguel", "orcid": "0000-0001-8054-0426" }, + { + "name": "Haehn, Daniel" + }, { "name": "Weinstein, Alejandro" }, @@ -587,11 +592,6 @@ "affiliation": "MIT, HMS", "name": "Ghosh, Satrajit", "orcid": "0000-0002-5312-6729" - }, - { - "affiliation": "GIGA Institute", - "name": "Grignard, Martin", - "orcid": "0000-0001-5549-1861" } ], "keywords": [ From 47fad80c943884e45a7fddb8402f5d9a04cd7dc3 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 26 Nov 2018 09:57:51 -0500 Subject: [PATCH 05/10] FIX: Numpy dependency --- nipype/info.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/nipype/info.py b/nipype/info.py index ff0a36e62c..8a3363cbfd 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -101,9 +101,10 @@ def get_nipype_gitversion(): # versions NIBABEL_MIN_VERSION = '2.1.0' NETWORKX_MIN_VERSION = '1.9' +NUMPY_MIN_VERSION = '1.9.0' # Numpy bug in python 3.7: # https://www.opensourceanswers.com/blog/you-shouldnt-use-python-37-for-data-science-right-now.html -NUMPY_MIN_VERSION = '1.9.0' if sys.version_info < (3, 7) else '1.15.4' +NUMPY_MIN_VERSION_37 = '1.15.3' SCIPY_MIN_VERSION = '0.14' TRAITS_MIN_VERSION = '4.6' DATEUTIL_MIN_VERSION = '2.2' @@ -136,6 +137,7 @@ def get_nipype_gitversion(): 'nibabel>=%s' % NIBABEL_MIN_VERSION, 'networkx>=%s' % NETWORKX_MIN_VERSION, 'numpy>=%s' % NUMPY_MIN_VERSION, + 'numpy>=%s ; python_version >= "3.7"' % NUMPY_MIN_VERSION_37, 'python-dateutil>=%s' % DATEUTIL_MIN_VERSION, 'scipy>=%s' % SCIPY_MIN_VERSION, 'traits>=%s' % TRAITS_MIN_VERSION, From 0076a896e8f4b39ce39b7b388e6cccbbfcbc50db Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 26 Nov 2018 10:07:08 -0500 Subject: [PATCH 06/10] CI: Test Numpy version under Python 3.7 --- .circleci/config.yml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 72bdd5056e..d2ee3cf717 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -1,5 +1,5 @@ _machine_kwds: &machine_kwds - image: circleci/classic:201710-02 + image: circleci/classic:201808-01 _store_artifacts_kwds: &store_artifacts_kwds path: /home/circleci/work/tests @@ -356,6 +356,13 @@ jobs: pip install dist/nipype-*-py2.py3-none-any.whl # Futures should not install in Python 3 test $(pip show futures 2>/dev/null | wc -l) = "0" + - run: + name: Validate Python 3.7 installation + command: | + pyenv local 3.7.0 + pip install dist/nipype-*-py2.py3-none-any.whl + # Futures should not install in Python 3 + test "$(pip show numpy | grep Version)" \> "Version: 1.15.2" - store_artifacts: path: /home/circleci/nipype/dist From 955a18c8ca68a5ef37df64de3c29d8cc78516f09 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 26 Nov 2018 11:13:05 -0500 Subject: [PATCH 07/10] MAINT: Make numpy min version explicitly for Python > 3.7 --- nipype/info.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/info.py b/nipype/info.py index 8a3363cbfd..4d034e75bc 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -136,7 +136,7 @@ def get_nipype_gitversion(): REQUIRES = [ 'nibabel>=%s' % NIBABEL_MIN_VERSION, 'networkx>=%s' % NETWORKX_MIN_VERSION, - 'numpy>=%s' % NUMPY_MIN_VERSION, + 'numpy>=%s ; python_version < "3.7"' % NUMPY_MIN_VERSION, 'numpy>=%s ; python_version >= "3.7"' % NUMPY_MIN_VERSION_37, 'python-dateutil>=%s' % DATEUTIL_MIN_VERSION, 'scipy>=%s' % SCIPY_MIN_VERSION, From 838f95e1e3bb4746a19fb52fc65fd21655769c7f Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 26 Nov 2018 11:14:07 -0500 Subject: [PATCH 08/10] CI: Update Python 3.7 install test --- .circleci/config.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index d2ee3cf717..c2356cebdf 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -360,8 +360,11 @@ jobs: name: Validate Python 3.7 installation command: | pyenv local 3.7.0 + pip install --upgrade pip + # Pre-install a version of numpy that will not pass + pip install numpy==1.15.0 pip install dist/nipype-*-py2.py3-none-any.whl - # Futures should not install in Python 3 + # Numpy should be upgraded to >= 1.15.3 test "$(pip show numpy | grep Version)" \> "Version: 1.15.2" - store_artifacts: path: /home/circleci/nipype/dist From 9851fe4f5f59ec976836537cb3570a38daa03d35 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 26 Nov 2018 11:24:56 -0500 Subject: [PATCH 09/10] DOC: Update changelog --- doc/changelog/1.X.X-changelog | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index 6882da62db..adf20cf8e9 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -1,10 +1,14 @@ 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) From 1de9f69859eb531b49edcc0ec29cb45f986a09ce Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 26 Nov 2018 11:32:58 -0500 Subject: [PATCH 10/10] MAINT: Remove pseudonym from zenodo --- .zenodo.json | 3 --- 1 file changed, 3 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 010329efb6..007a43c415 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -456,9 +456,6 @@ "name": "Durnez, Joke", "orcid": "0000-0001-9030-2202" }, - { - "name": "Mertz, Fred" - }, { "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry", "name": "Geisler, Daniel",