From 3d434707bb7aec708bb2ba6e08489cf60880ee7d Mon Sep 17 00:00:00 2001 From: mathiasg Date: Mon, 26 Mar 2018 10:17:23 -0400 Subject: [PATCH 1/5] REL: 1.0.2 --- .zenodo.json | 92 +++++++++++++++++------------------ doc/changelog/1.X.X-changelog | 22 +++++++++ doc/conf.py | 2 +- nipype/info.py | 2 +- tools/update_changes.sh | 10 ++-- 5 files changed, 76 insertions(+), 52 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 29e7f047ac..da7c45dbda 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -20,16 +20,16 @@ "name": "Ellis, David Gage", "orcid": "0000-0002-3718-6836" }, - { - "affiliation": "The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland", - "name": "Notter, Michael Philipp", - "orcid": "0000-0002-5866-047X" - }, { "affiliation": "Stanford University", "name": "Markiewicz, Christopher J.", "orcid": "0000-0002-6533-164X" }, + { + "affiliation": "The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland", + "name": "Notter, Michael Philipp", + "orcid": "0000-0002-5866-047X" + }, { "affiliation": "University of Iowa", "name": "Johnson, Hans", @@ -105,11 +105,6 @@ "name": "Dayan, Michael", "orcid": "0000-0002-2666-0969" }, - { - "affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering", - "name": "Keshavan, Anisha", - "orcid": "0000-0003-3554-043X" - }, { "affiliation": "UC Berkeley", "name": "Clark, Dav", @@ -120,6 +115,11 @@ "name": "Visconti di Oleggio Castello, Matteo", "orcid": "0000-0001-7931-5272" }, + { + "affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering", + "name": "Keshavan, Anisha", + "orcid": "0000-0003-3554-043X" + }, { "affiliation": "CNRS LTCI, Telecom ParisTech, Universit\u00e9 Paris-Saclay", "name": "Gramfort, Alexandre", @@ -156,14 +156,18 @@ "name": "Rokem, Ariel", "orcid": "0000-0003-0679-1985" }, + { + "name": "Moloney, Brendan" + }, + { + "affiliation": "Molecular Imaging Research Center, CEA, France", + "name": "Bougacha, Salma" + }, { "affiliation": "Athena EPI, Inria Sophia-Antipolis", "name": "Wassermann , Demian", "orcid": "0000-0001-5194-6056" }, - { - "name": "Moloney, Brendan" - }, { "affiliation": "Dartmouth College: Hanover, NH, United States", "name": "Halchenko, Yaroslav O.", @@ -179,10 +183,6 @@ "name": "Horea, Christian", "orcid": "0000-0001-7037-2449" }, - { - "affiliation": "Molecular Imaging Research Center, CEA, France", - "name": "Bougacha, Salma" - }, { "affiliation": "MIT", "name": "Kaczmarzyk, Jakub", @@ -193,6 +193,16 @@ "name": "Gilles de Hollander", "orcid": "0000-0003-1988-5091" }, + { + "affiliation": "Montreal Neurological Institute and Hospital", + "name": "DuPre, Elizabeth", + "orcid": "0000-0003-1358-196X" + }, + { + "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" }, @@ -229,11 +239,6 @@ "name": "Malone, Ian B.", "orcid": "0000-0001-7512-7856" }, - { - "affiliation": "Montreal Neurological Institute and Hospital", - "name": "DuPre, Elizabeth", - "orcid": "0000-0003-1358-196X" - }, { "name": "Dubois, Mathieu" }, @@ -259,11 +264,6 @@ "name": "Huntenburg, Julia M.", "orcid": "0000-0003-0579-9811" }, - { - "affiliation": "University College London", - "name": "Eshaghi, Arman", - "orcid": "0000-0002-6652-3512" - }, { "affiliation": "Harvard University - Psychology", "name": "Kastman, Erik", @@ -274,6 +274,11 @@ "name": "Nichols, B. Nolan", "orcid": "0000-0003-1099-3328" }, + { + "affiliation": "University College London", + "name": "Eshaghi, Arman", + "orcid": "0000-0002-6652-3512" + }, { "name": "Ginsburg, Daniel" }, @@ -290,11 +295,6 @@ { "name": "Kent, James" }, - { - "affiliation": "Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation; University of Queensland", - "name": "Gillman, Ashley", - "orcid": "0000-0001-9130-1092" - }, { "affiliation": "Child Mind Institute", "name": "Giavasis, Steven" @@ -356,6 +356,11 @@ "name": "Kahn, Ari E.", "orcid": "0000-0002-2127-0507" }, + { + "affiliation": "University College London", + "name": "P\u00e9rez-Garc\u00eda, Fernando", + "orcid": "0000-0001-9090-3024" + }, { "affiliation": "Department of Psychology, Stanford University", "name": "Triplett, William", @@ -384,9 +389,6 @@ { "name": "Salvatore, John" }, - { - "name": "Mertz, Fred" - }, { "name": "Park, Anne" }, @@ -409,11 +411,6 @@ { "name": "Hinds, Oliver" }, - { - "affiliation": "Technical University Munich", - "name": "Molina-Romero, Miguel", - "orcid": "0000-0001-8054-0426" - }, { "affiliation": "University of Newcastle, Australia", "name": "Cooper, Gavin", @@ -467,6 +464,9 @@ "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", @@ -476,14 +476,15 @@ "affiliation": "The University of Texas at Austin", "name": "Floren, Andrew", "orcid": "0000-0003-3618-2056" - }, + }, { "affiliation": "University of illinois urbana champaign", "name": "Sharp, Paul" }, { - "affiliation": "Vrije Universiteit Amsterdam", - "name": "Ort, Eduard" + "affiliation": "Technical University Munich", + "name": "Molina-Romero, Miguel", + "orcid": "0000-0001-8054-0426" }, { "name": "Weinstein, Alejandro" @@ -558,9 +559,8 @@ "name": "Flandin, Guillaume" }, { - "affiliation": "University College London", - "name": "P\u00e9rez-Garc\u00eda, Fernando", - "orcid": "0000-0001-9090-3024" + "affiliation": "Vrije Universiteit Amsterdam", + "name": "Ort, Eduard" }, { "name": "Shachnev, Dmitry" diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index 49b8790ff9..c7fee5c7ac 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -1,3 +1,25 @@ +1.0.2 (March 26, 2018) +====================== + +###### [Full changelog](https://github.com/nipy/nipype/milestone/16?closed=1) + + * FIX: dcm2niix interface (https://github.com/nipy/nipype/pull/2498) + * FIX: mark .niml.dset as special extension in utils.filemanip (https://github.com/nipy/nipype/pull/2495) + * FIX: handle automatic module creation, name extraction, default value (https://github.com/nipy/nipype/pull/2490) + * FIX: Check and report mount table parsing failures (https://github.com/nipy/nipype/pull/2476) + * FIX: Check against full node name when reconnecting JoinNodes (https://github.com/nipy/nipype/pull/2479) + * DOC: Add tutorials, porcupine to users TOC (https://github.com/nipy/nipype/pull/2503 + * DOC: Contributing and testing (https://github.com/nipy/nipype/pull/2482) + * DOC: Describe 'orphaned' tag in CONTRIBUTING (https://github.com/nipy/nipype/pull/2481) + * ENH: Afni nwarpadjust (https://github.com/nipy/nipype/pull/2450) + * ENH: Update SSHDataGrabber to fetch related files (https://github.com/nipy/nipype/pull/2104) + * ENH: Add interpolation order parameter to NiftyReg's RegTools (https://github.com/nipy/nipype/pull/2471) + * MAINT: Stray warnings and exceptions (https://github.com/nipy/nipype/pull/2478) + * MAINT: Add dev install option, update CONTRIBUTING (https://github.com/nipy/nipype/pull/2477) + * MAINT: Sync requirements with info.py (https://github.com/nipy/nipype/pull/2472) + * CI: Update Travis builds, Docker to use latest miniconda (https://github.com/nipy/nipype/pull/2455) + * TEST: Parallelize pytest (https://github.com/nipy/nipype/pull/2469) + 1.0.1 (February 27, 2018) ========================= diff --git a/doc/conf.py b/doc/conf.py index c0c66cbc1e..f19df6872d 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 = "1.0.1" +release = "1.0.2" # 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 9438567ff3..6c8412df51 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__ = '1.0.2-dev' +__version__ = '1.0.2' def get_nipype_gitversion(): diff --git a/tools/update_changes.sh b/tools/update_changes.sh index 9327118c7a..017c0623f2 100644 --- a/tools/update_changes.sh +++ b/tools/update_changes.sh @@ -12,8 +12,10 @@ set -u # Treat unset variables as an error when substituting. set -x # Print command traces before executing command. +CHANGES=../doc/changelog/1.X.X-changelog + # Check whether the Upcoming release header is present -head -1 CHANGES | grep -q Upcoming +head -1 $CHANGES | grep -q Upcoming UPCOMING=$? # Elaborate today's release header @@ -30,11 +32,11 @@ echo "" >> newchanges # Append old CHANGES if [[ "$UPCOMING" == "0" ]]; then # Drop the Upcoming title if present - tail -n+4 CHANGES >> newchanges + tail -n+4 $CHANGES >> newchanges else - cat CHANGES >> newchanges + cat $CHANGES >> newchanges fi # Replace old CHANGES with new file -mv newchanges CHANGES +mv newchanges $CHANGES From aecb5594c59e0481da7de9e315e09bc4a8f4f160 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Mon, 26 Mar 2018 15:08:40 -0400 Subject: [PATCH 2/5] DOC: More informative changelog entry [skip ci] --- doc/changelog/1.X.X-changelog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index c7fee5c7ac..593d753e51 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -11,7 +11,7 @@ * DOC: Add tutorials, porcupine to users TOC (https://github.com/nipy/nipype/pull/2503 * DOC: Contributing and testing (https://github.com/nipy/nipype/pull/2482) * DOC: Describe 'orphaned' tag in CONTRIBUTING (https://github.com/nipy/nipype/pull/2481) - * ENH: Afni nwarpadjust (https://github.com/nipy/nipype/pull/2450) + * ENH: Add interface for AFNI 3dNwarpAdjust (https://github.com/nipy/nipype/pull/2450) * ENH: Update SSHDataGrabber to fetch related files (https://github.com/nipy/nipype/pull/2104) * ENH: Add interpolation order parameter to NiftyReg's RegTools (https://github.com/nipy/nipype/pull/2471) * MAINT: Stray warnings and exceptions (https://github.com/nipy/nipype/pull/2478) From 9d58f6db6897fc1f925177d8a9e2c1d9fba56aa0 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 27 Mar 2018 09:36:14 -0400 Subject: [PATCH 3/5] TEST: Get string paths for test files Closes gh-2513 --- nipype/algorithms/tests/test_mesh_ops.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/nipype/algorithms/tests/test_mesh_ops.py b/nipype/algorithms/tests/test_mesh_ops.py index 53eec75b69..a08a5a97c3 100644 --- a/nipype/algorithms/tests/test_mesh_ops.py +++ b/nipype/algorithms/tests/test_mesh_ops.py @@ -21,7 +21,7 @@ def test_ident_distances(tmpdir): dist_ident = m.ComputeMeshWarp() dist_ident.inputs.surface1 = in_surf dist_ident.inputs.surface2 = in_surf - dist_ident.inputs.out_file = tmpdir.join('distance.npy') + dist_ident.inputs.out_file = tmpdir.join('distance.npy').strpath res = dist_ident.run() assert res.outputs.distance == 0.0 @@ -35,7 +35,7 @@ def test_trans_distances(tmpdir): from ...interfaces.vtkbase import tvtk in_surf = example_data('surf01.vtk') - warped_surf = tmpdir.join('warped.vtk') + warped_surf = tmpdir.join('warped.vtk').strpath inc = np.array([0.7, 0.3, -0.2]) @@ -51,7 +51,7 @@ def test_trans_distances(tmpdir): dist = m.ComputeMeshWarp() dist.inputs.surface1 = in_surf dist.inputs.surface2 = warped_surf - dist.inputs.out_file = tmpdir.join('distance.npy') + dist.inputs.out_file = tmpdir.join('distance.npy').strpath res = dist.run() assert np.allclose(res.outputs.distance, np.linalg.norm(inc), 4) dist.inputs.weighting = 'area' From 2861ec305a5edf820c33b7306de7d037e67ca999 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 27 Mar 2018 09:42:48 -0400 Subject: [PATCH 4/5] DOC: Update changelog --- doc/changelog/1.X.X-changelog | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index 593d753e51..56a7fae652 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -11,6 +11,7 @@ * DOC: Add tutorials, porcupine to users TOC (https://github.com/nipy/nipype/pull/2503 * DOC: Contributing and testing (https://github.com/nipy/nipype/pull/2482) * DOC: Describe 'orphaned' tag in CONTRIBUTING (https://github.com/nipy/nipype/pull/2481) + * DOC: Add details for dcm2niix output filename pattern (https://github.com/nipy/nipype/pull/2512) * ENH: Add interface for AFNI 3dNwarpAdjust (https://github.com/nipy/nipype/pull/2450) * ENH: Update SSHDataGrabber to fetch related files (https://github.com/nipy/nipype/pull/2104) * ENH: Add interpolation order parameter to NiftyReg's RegTools (https://github.com/nipy/nipype/pull/2471) From 41baf0f5a2679c96c30a47dc70fd82cc20d2608c Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 27 Mar 2018 11:26:04 -0400 Subject: [PATCH 5/5] DOC: Fix date [skip ci] --- doc/changelog/1.X.X-changelog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index 56a7fae652..717e83ce03 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -1,4 +1,4 @@ -1.0.2 (March 26, 2018) +1.0.2 (March 27, 2018) ====================== ###### [Full changelog](https://github.com/nipy/nipype/milestone/16?closed=1)