From 6b996c0e2c06dd4e6220bf9d1591101e75552b78 Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 5 Sep 2019 10:55:09 -0700 Subject: [PATCH 1/9] rel(1.2.2): Update changelog --- doc/changelog/1.X.X-changelog | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index 9ef4474bf1..2d749b758b 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -1,3 +1,13 @@ +1.2.2 (September 05, 2019) +========================== + + * FIX: Update mne.WatershedBEM command line (https://github.com/nipy/nipype/pull/3007) + * FIX: Specify correct stop criterion flag in PETPVC (https://github.com/nipy/nipype/pull/3010) + * ENH: Additional arguments to ANTs N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3012) + * ENH: Add ``--rescale-intensities`` and name_source to N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3011) + * ENH: Add index_mask_file input to ImageStats (https://github.com/nipy/nipype/pull/3005) + * MAINT: Add ``python_requires`` to package metadata (https://github.com/nipy/nipype/pull/3006) + 1.2.1 (August 19, 2019) ======================= From 5f028b3e6c87ceaba8e592718b5c54b8d2aa952d Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 5 Sep 2019 11:05:07 -0700 Subject: [PATCH 2/9] rel(1.2.2): Update .mailmap --- .mailmap | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.mailmap b/.mailmap index 259fbe170d..2ffec2dcef 100644 --- a/.mailmap +++ b/.mailmap @@ -151,6 +151,7 @@ Michael Waskom mwaskom Michael Waskom mwaskom Michael Waskom mwaskom Miguel Molina-Romero Miguel Molina +Murat Bilgel Murat Bilgel Oliver Contier oliver-contier Oscar Esteban Oscar Esteban Oscar Esteban oesteban @@ -159,7 +160,7 @@ Pablo Polosecki pipolose psharp1289 Ranjit Khanuja RanjitK Rastko Ćirić rciric -Rastko Ćirić Rastko Ćirić +Rastko Ćirić Rastko Ćirić rciric Ross Markello Ross Markello Russell Poldrack Russ Poldrack Russell Poldrack poldrack @@ -182,7 +183,9 @@ Siqi Liu sql Steven Giavasis Steven Giavasis Steven Giavasis sgiavasis Steven Giavasis sgiavasis +Steven Tilley Steven Tilley Tristan Glatard Tristan Glatard +Victor Férat Victor Victor Ferat Victor Férat Victor Saase vsaase Weijie Huang forwho William Triplett William Triplett From 3428c8a45ecf060f6105ebf32ba6e7d2219b2061 Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 5 Sep 2019 11:36:53 -0700 Subject: [PATCH 3/9] rel(1.2.2): Update ``.zenodo.json`` MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Output of ``python tools/update_zenodo.py``: ``` No entry to sort: Victor Férat No entry to sort: Martin No entry to sort: Isaiah Norton No entry to sort: Niklas Förster No entry to sort: daniel glen No entry to sort: rciric No entry to sort: Kirstie Whitaker No entry to sort: hstojic No entry to sort: Gio Piantoni No entry to sort: Jonathan R. Williford No entry to sort: Hao No entry to sort: Fred Mertz No entry to sort: Murat Bilgel No entry to sort: Kevin Sitek No entry to sort: Ami Tsuchida No entry to sort: Abel González No entry to sort: Michiel Cottaar No entry to sort: Daniel Brenner ``` --- .zenodo.json | 71 +++++++++++++++++++++++++--------------------------- 1 file changed, 34 insertions(+), 37 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index bf1cb6f692..c1567cf65d 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -78,10 +78,6 @@ "affiliation": "Shattuck Lab, UCLA Brain Mapping Center", "name": "Wong, Jason" }, - { - "affiliation": "Concordia University", - "name": "Benderoff, Erin" - }, { "name": "Modat, Marc" }, @@ -150,6 +146,10 @@ { "name": "Berleant, Shoshana" }, + { + "affiliation": "Concordia University", + "name": "Benderoff, Erin" + }, { "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich", "name": "Christian, Horea", @@ -355,15 +355,15 @@ { "name": "Erickson, Drew" }, - { - "affiliation": "Child Mind Institute", - "name": "Giavasis, Steven" - }, { "affiliation": "NIMH IRP", "name": "Lee, John A.", "orcid": "0000-0001-5884-4247" }, + { + "affiliation": "Child Mind Institute", + "name": "Giavasis, Steven" + }, { "name": "Correa, Carlos" }, @@ -381,9 +381,6 @@ { "name": "Millman, Jarrod" }, - { - "name": "Lai, Jeff" - }, { "name": "Zhou, Dale" }, @@ -400,16 +397,16 @@ "affiliation": "The University of Sydney", "name": "Liu, Siqi" }, - { - "affiliation": "Leibniz Institute for Neurobiology", - "name": "Stadler, J\u00f6rg", - "orcid": "0000-0003-4313-129X" - }, { "affiliation": "University of Pennsylvania", "name": "Kahn, Ari E.", "orcid": "0000-0002-2127-0507" }, + { + "affiliation": "Leibniz Institute for Neurobiology", + "name": "Stadler, J\u00f6rg", + "orcid": "0000-0003-4313-129X" + }, { "affiliation": "University College London", "name": "P\u00e9rez-Garc\u00eda, Fernando", @@ -432,6 +429,11 @@ { "name": "Hallquist, Michael" }, + { + "affiliation": "Holland Bloorview Kids Rehabilitation Hospital", + "name": "Tilley II, Steven", + "orcid": "0000-0003-4853-5082" + }, { "affiliation": "Yale University; New Haven, CT, United States", "name": "Sisk, Lucinda M.", @@ -502,31 +504,26 @@ "name": "Perkins, L. Nathan" }, { - "affiliation": "University of Amsterdam", - "name": "Lukas Snoek", - "orcid": "0000-0001-8972-204X" + "name": "Marina, Ana" }, { - "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany", - "name": "Weninger, Leon" + "name": "Mattfeld, Aaron" }, { - "affiliation": "Stanford University", - "name": "Lerma-Usabiaga, Garikoitz", - "orcid": "0000-0001-9800-4816" + "name": "Noel, Maxime" }, { - "name": "Marina, Ana" + "affiliation": "University of Amsterdam", + "name": "Lukas Snoek", + "orcid": "0000-0001-8972-204X" }, { - "name": "Mattfeld, Aaron" + "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany", + "name": "Weninger, Leon" }, { "name": "Matsubara, K" }, - { - "name": "Noel, Maxime" - }, { "name": "Cheung, Brian" }, @@ -573,9 +570,6 @@ { "name": "Weinstein, Alejandro" }, - { - "name": "Tambini, Arielle" - }, { "affiliation": "Duke University", "name": "Broderick, William", @@ -612,6 +606,9 @@ { "name": "Tarbert, Claire" }, + { + "name": "Tambini, Arielle" + }, { "name": "Nickson, Thomas" }, @@ -636,6 +633,11 @@ { "name": "Flandin, Guillaume" }, + { + "affiliation": "Stanford University", + "name": "Lerma-Usabiaga, Garikoitz", + "orcid": "0000-0001-9800-4816" + }, { "affiliation": "Vrije Universiteit Amsterdam", "name": "Ort, Eduard" @@ -695,11 +697,6 @@ "affiliation": "MIT, HMS", "name": "Ghosh, Satrajit", "orcid": "0000-0002-5312-6729" - }, - { - "affiliation": "Holland Bloorview Kids Rehabilitation Hospital", - "name": "Tilley II, Steven", - "orcid": "0000-0003-4853-5082" } ], "keywords": [ From 968a76f0887996da853542ec5baed62cce1348f0 Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 5 Sep 2019 11:39:48 -0700 Subject: [PATCH 4/9] rel(1.2.2): Update version in ``nipype/info.py`` and ``doc/conf.py`` --- doc/conf.py | 2 +- nipype/info.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 2a253eb7aa..bdf938a70c 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 = "1.2.1" +release = "1.2.2" # 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 827bc93a12..7c13e94418 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -9,7 +9,7 @@ # nipype version information # Remove -dev for release -__version__ = '1.2.2-dev' +__version__ = '1.2.2' def get_nipype_gitversion(): From 7df091d2689700801aeeb7ed75e9e7515c2906d9 Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 5 Sep 2019 12:15:02 -0700 Subject: [PATCH 5/9] rel(1.2.2): revise problems spotted by @effigies' --- .mailmap | 7 +++++-- .zenodo.json | 3 +++ doc/changelog/1.X.X-changelog | 2 ++ tools/update_zenodo.py | 1 + 4 files changed, 11 insertions(+), 2 deletions(-) diff --git a/.mailmap b/.mailmap index 2ffec2dcef..946919557c 100644 --- a/.mailmap +++ b/.mailmap @@ -160,7 +160,8 @@ Pablo Polosecki pipolose psharp1289 Ranjit Khanuja RanjitK Rastko Ćirić rciric -Rastko Ćirić Rastko Ćirić rciric +Rastko Ćirić Rastko Ćirić +Rastko Ćirić rciric Ross Markello Ross Markello Russell Poldrack Russ Poldrack Russell Poldrack poldrack @@ -185,7 +186,9 @@ Steven Giavasis sgiavasis Steven Giavasis sgiavasis Steven Tilley Steven Tilley Tristan Glatard Tristan Glatard -Victor Férat Victor Victor Ferat Victor Férat +Victor Férat Victor +Victor Férat Victor Ferat +Victor Férat Victor Férat Victor Saase vsaase Weijie Huang forwho William Triplett William Triplett diff --git a/.zenodo.json b/.zenodo.json index c1567cf65d..8d72952ade 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -693,6 +693,9 @@ "name": "Mihai, Paul Glad", "orcid": "0000-0001-5715-6442" }, + { + "name": "Lai, Jeff" + }, { "affiliation": "MIT, HMS", "name": "Ghosh, Satrajit", diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index 2d749b758b..843fe5a209 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -1,6 +1,8 @@ 1.2.2 (September 05, 2019) ========================== +##### [Full changelog](https://github.com/nipy/nipype/milestone/33?closed=1) + * FIX: Update mne.WatershedBEM command line (https://github.com/nipy/nipype/pull/3007) * FIX: Specify correct stop criterion flag in PETPVC (https://github.com/nipy/nipype/pull/3010) * ENH: Additional arguments to ANTs N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3012) diff --git a/tools/update_zenodo.py b/tools/update_zenodo.py index 637defad49..163f88084d 100755 --- a/tools/update_zenodo.py +++ b/tools/update_zenodo.py @@ -58,6 +58,7 @@ "Leipzig, Germany.", "name": "Mihai, Paul Glad", "orcid": "0000-0001-5715-6442"}, + {"name": "Lai, Jeff"} ] for entry in missing_entries: From 4ac9ecd68ed938a97de400507396e248ffcbf75c Mon Sep 17 00:00:00 2001 From: Murat Bilgel Date: Thu, 5 Sep 2019 15:17:31 -0400 Subject: [PATCH 6/9] rel(1.2.2): Add @bilgelm to ``.zenodo.json``, cherry-picking e520a8832 --- .zenodo.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.zenodo.json b/.zenodo.json index 8d72952ade..f0ae25659e 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -592,6 +592,11 @@ { "name": "Khanuja, Ranjeet" }, + { + "affiliation": "National Institute on Aging, Baltimore, MD, USA", + "name": "Bilgel, Murat", + "orcid": "0000-0001-5042-7422" + }, { "name": "Schlamp, Kai" }, From 875c75c907bb89ed4d908c1a5da15d257b5e5a23 Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 5 Sep 2019 23:50:58 -0700 Subject: [PATCH 7/9] rel(1.2.2): update .zenodo.json --- .zenodo.json | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index f0ae25659e..1850eec791 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -390,6 +390,11 @@ { "name": "Haselgrove, Christian" }, + { + "affiliation": "Holland Bloorview Kids Rehabilitation Hospital", + "name": "Tilley II, Steven", + "orcid": "0000-0003-4853-5082" + }, { "name": "Renfro, Mandy" }, @@ -429,11 +434,6 @@ { "name": "Hallquist, Michael" }, - { - "affiliation": "Holland Bloorview Kids Rehabilitation Hospital", - "name": "Tilley II, Steven", - "orcid": "0000-0003-4853-5082" - }, { "affiliation": "Yale University; New Haven, CT, United States", "name": "Sisk, Lucinda M.", From b61585f733ee6cadc699648059c70a9351e1baec Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 5 Sep 2019 23:54:21 -0700 Subject: [PATCH 8/9] rel(1.2.2): 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 843fe5a209..eae851279a 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/33?closed=1) + * FIX: ``loadpkl`` failed when pklz file contained versioning info (https://github.com/nipy/nipype/pull/3017) * FIX: Update mne.WatershedBEM command line (https://github.com/nipy/nipype/pull/3007) * FIX: Specify correct stop criterion flag in PETPVC (https://github.com/nipy/nipype/pull/3010) * ENH: Additional arguments to ANTs N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3012) From 5f8be53fa72475e8371b48e548fdedf01a01e3b3 Mon Sep 17 00:00:00 2001 From: oesteban Date: Fri, 6 Sep 2019 14:41:06 -0700 Subject: [PATCH 9/9] rel(1.2.2): 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 eae851279a..014c1485d0 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/33?closed=1) + * FIX: Ensure ``loadpkl`` returns a not None value (https://github.com/nipy/nipype/pull/3020) * FIX: ``loadpkl`` failed when pklz file contained versioning info (https://github.com/nipy/nipype/pull/3017) * FIX: Update mne.WatershedBEM command line (https://github.com/nipy/nipype/pull/3007) * FIX: Specify correct stop criterion flag in PETPVC (https://github.com/nipy/nipype/pull/3010)