From 9dbcf9769f69ed0d01f282e9441235d57f744daa Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Fri, 27 Jul 2018 09:33:08 -0400 Subject: [PATCH 1/5] REL: 1.1.1 prep --- doc/changelog/1.X.X-changelog | 19 +++++++++++++++++++ doc/conf.py | 2 +- nipype/info.py | 2 +- 3 files changed, 21 insertions(+), 2 deletions(-) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index b34ed5cb19..b33621896f 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -1,3 +1,22 @@ +1.1.1 (July 30, 2018) +===================== + +##### [Full changelog](https://github.com/nipy/nipype/milestone/22?closed=1) + + * FIX: Copy FSCommand.version to ReconAll.version (https://github.com/nipy/nipype/pull/2656) + * FIX: Various BIDSDataGrabber fixes (https://github.com/nipy/nipype/pull/2651) + * FIX: changing Node._output_dir to realpath (https://github.com/nipy/nipype/pull/2639) + * FIX: Typo in DWIExtract of Mrtrix3interface (https://github.com/nipy/nipype/pull/2634) + * FIX: Typo in FSLXCommandInputSpec (https://github.com/nipy/nipype/pull/2628) + * ENH: Allow transform to be saved from AFNI 3dWarp (https://github.com/nipy/nipype/pull/2642) + * ENH: Allow BIDS-style slice timings to be passed directly to TShift (https://github.com/nipy/nipype/pull/2608) + * ENH: S3 access using instance role (https://github.com/nipy/nipype/pull/2621) + * ENH Minor improvements to PR template (https://github.com/nipy/nipype/pull/2636) + * TEST: make specs (https://github.com/nipy/nipype/pull/2653) + * DOC: update neurodocker tutorial for neurodocker version 0.4.0 (https://github.com/nipy/nipype/pull/2647) + * MAINT: Make pytest-xdist a dependency (https://github.com/nipy/nipype/pull/2649) + + 1.1.0 (July 04, 2018) ===================== diff --git a/doc/conf.py b/doc/conf.py index 1af17976b5..2278981f47 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 = "1.1.0" +release = "1.1.1" # 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 6b60da6603..f4f1e51623 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__ = '1.1.1-dev' +__version__ = '1.1.1' def get_nipype_gitversion(): From 9484c4947812640cb3fa5d1f73c7e423f22ac78b Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Fri, 27 Jul 2018 14:46:33 -0400 Subject: [PATCH 2/5] DOC: Update changelog --- doc/changelog/1.X.X-changelog | 3 +++ 1 file changed, 3 insertions(+) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index b33621896f..18e4598f94 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -3,6 +3,7 @@ ##### [Full changelog](https://github.com/nipy/nipype/milestone/22?closed=1) + * FIX: Un-set incorrect default options in TOPUP (https://github.com/nipy/nipype/pull/2637) * FIX: Copy FSCommand.version to ReconAll.version (https://github.com/nipy/nipype/pull/2656) * FIX: Various BIDSDataGrabber fixes (https://github.com/nipy/nipype/pull/2651) * FIX: changing Node._output_dir to realpath (https://github.com/nipy/nipype/pull/2639) @@ -14,7 +15,9 @@ * ENH Minor improvements to PR template (https://github.com/nipy/nipype/pull/2636) * TEST: make specs (https://github.com/nipy/nipype/pull/2653) * DOC: update neurodocker tutorial for neurodocker version 0.4.0 (https://github.com/nipy/nipype/pull/2647) + * MAINT: Remove vestiges of nose testing library (https://github.com/nipy/nipype/pull/2662) * MAINT: Make pytest-xdist a dependency (https://github.com/nipy/nipype/pull/2649) + * CI: Install pytest>=3.4 in Travis (https://github.com/nipy/nipype/pull/2659) 1.1.0 (July 04, 2018) From 99970decd0f0ef2354f2bf2003ebeba706f745f9 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Fri, 27 Jul 2018 15:19:26 -0400 Subject: [PATCH 3/5] doc: update previous releases --- doc/documentation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/documentation.rst b/doc/documentation.rst index 73ba89d233..06690ccc90 100644 --- a/doc/documentation.rst +++ b/doc/documentation.rst @@ -9,7 +9,7 @@ Documentation :Release: |version| :Date: |today| -Previous versions: `1.0.3 `_ `1.0.2 `_ +Previous versions: `1.1.0 `_ `1.0.4 `_ .. container:: doc2 From 0ccb6b377cdda9c5c7e77762979ed521d11f146b Mon Sep 17 00:00:00 2001 From: mathiasg Date: Fri, 27 Jul 2018 15:19:43 -0400 Subject: [PATCH 4/5] doc: zenodo updates --- .zenodo.json | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index bd6d39d56a..51e0460509 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -30,16 +30,16 @@ "name": "Notter, Michael Philipp", "orcid": "0000-0002-5866-047X" }, - { - "affiliation": "MIT", - "name": "Jarecka, Dorota", - "orcid": "0000-0003-1857-8129" - }, { "affiliation": "University of Iowa", "name": "Johnson, Hans", "orcid": "0000-0001-9513-2660" }, + { + "affiliation": "MIT", + "name": "Jarecka, Dorota", + "orcid": "0000-0003-1857-8129" + }, { "name": "Burns, Christopher" }, @@ -60,16 +60,16 @@ "name": "Salo, Taylor", "orcid": "0000-0001-9813-3167" }, - { - "affiliation": "University of California, San Francisco", - "name": "Jordan, Kesshi", - "orcid": "0000-0001-6313-0580" - }, { "affiliation": "MIT", "name": "Goncalves, Mathias", "orcid": "0000-0002-7252-7771" }, + { + "affiliation": "University of California, San Francisco", + "name": "Jordan, Kesshi", + "orcid": "0000-0001-6313-0580" + }, { "affiliation": "Department of Psychology, Stanford University", "name": "Waskom, Michael" @@ -151,6 +151,11 @@ "name": "Cipollini, Ben", "orcid": "0000-0002-7782-0790" }, + { + "affiliation": "Dartmouth College: Hanover, NH, United States", + "name": "Halchenko, Yaroslav O.", + "orcid": "0000-0003-3456-2493" + }, { "affiliation": "Montreal Neurological Institute and Hospital", "name": "Markello, Ross", @@ -164,11 +169,6 @@ { "name": "Moloney, Brendan" }, - { - "affiliation": "Dartmouth College: Hanover, NH, United States", - "name": "Halchenko, Yaroslav O.", - "orcid": "0000-0003-3456-2493" - }, { "affiliation": "Athena EPI, Inria Sophia-Antipolis", "name": "Wassermann , Demian", @@ -325,9 +325,6 @@ { "name": "Millman, Jarrod" }, - { - "name": "Haehn, Daniel" - }, { "name": "Lai, Jeff" }, @@ -449,6 +446,9 @@ { "name": "Mertz, Fred" }, + { + "name": "Haehn, Daniel" + }, { "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry", "name": "Geisler, Daniel", From 73a2e1b59cc02763fa2e457e9fe110e524f1edd7 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 30 Jul 2018 09:54:02 -0400 Subject: [PATCH 5/5] STY: Cleanup --- nipype/interfaces/ants/registration.py | 2 +- nipype/interfaces/io.py | 2 +- nipype/utils/filemanip.py | 2 +- nipype/utils/tests/test_filemanip.py | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py index 7190816cf3..9d3b07e96a 100644 --- a/nipype/interfaces/ants/registration.py +++ b/nipype/interfaces/ants/registration.py @@ -125,7 +125,7 @@ class ANTSOutputSpec(TraitedSpec): class ANTS(ANTSCommand): - """ANTS wrapper for registration of images + """ANTS wrapper for registration of images (old, use Registration instead) Examples diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index 7a89675e8d..5a806a67be 100644 --- a/nipype/interfaces/io.py +++ b/nipype/interfaces/io.py @@ -124,7 +124,7 @@ def add_traits(base, names, trait_type=None): def _get_head_bucket(s3_resource, bucket_name): - """ Try to get the header info of a bucket, in order to + """ Try to get the header info of a bucket, in order to check if it exists and its permissions """ diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py index 80fc262f03..8bf4c456d2 100644 --- a/nipype/utils/filemanip.py +++ b/nipype/utils/filemanip.py @@ -662,7 +662,7 @@ def loadpkl(infile, versioning=False): return unpkl - # Unpickling problems + # Unpickling problems except Exception as e: if not versioning: raise e diff --git a/nipype/utils/tests/test_filemanip.py b/nipype/utils/tests/test_filemanip.py index ae5316c7d7..b9a413d557 100644 --- a/nipype/utils/tests/test_filemanip.py +++ b/nipype/utils/tests/test_filemanip.py @@ -547,7 +547,7 @@ class PickledBreaker: def __setstate__(self, d): raise Exception() - + def test_versioned_pklization(tmpdir): tmpdir.chdir() @@ -560,7 +560,7 @@ def test_versioned_pklization(tmpdir): loadpkl('./pickled.pkz', versioning=True) - + def test_unversioned_pklization(tmpdir): tmpdir.chdir()