From a7124255c0aa944100f63559382f25542429882b Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 7 Oct 2019 16:39:59 -0400 Subject: [PATCH 1/8] DOC: Update changelog --- doc/changelog/1.X.X-changelog | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index 82747d9903..cfac06b090 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -1,3 +1,22 @@ +1.3.0 (To Be Determined) +======================== + +##### [Full changelog](https://github.com/nipy/nipype/milestone/34?closed=1) + + * FIX: Restore ``AFNICommand._get_fname``, required by some interfaces (https://github.com/nipy/nipype/pull/3071) + * FIX: Remove asynchronous chdir callback (https://github.com/nipy/nipype/pull/3060) + * FIX: Minimize scope for directory changes while loading results file (https://github.com/nipy/nipype/pull/3061) + * ENH: Add precommit information for contributors and pre-commit style (https://github.com/nipy/nipype/pull/3063) + * ENH: Delay etelemetry for non-interactive sessions, report bad versions (https://github.com/nipy/nipype/pull/3049) + * ENH: Run memoized check_version at REPL import, Node/Workflow/Interface init (https://github.com/nipy/nipype/pull/30) + * RF: Provide functions to augment old Path.mkdir, Path.resolve methods (https://github.com/nipy/nipype/pull/3050) + * RF: Redirect nipype.workflows to niflow.nipype1.workflows (https://github.com/nipy/nipype/pull/3067) + * TST: Skip dcm2niix test if data fails to download (https://github.com/nipy/nipype/pull/3059) + * TST: dcm2niix test fix (https://github.com/nipy/nipype/pull/3058) + * MAINT: Drop Python 3.4 support (https://github.com/nipy/nipype/pull/3062) + * CI: ``make specs`` on Travis (https://github.com/nipy/nipype/pull/3066) + + 1.2.3 (September 23, 2019) ========================== From 040b94270d708cf0945698f9e88bb04bef849ffc Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 7 Oct 2019 16:41:11 -0400 Subject: [PATCH 2/8] MNT: Version 1.3.0-rc1 --- 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 10ac3c36db..c49f20e514 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 = "1.2.3" +release = "1.3.0-rc1" # 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 9ba12193ea..aa8f460688 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -9,7 +9,7 @@ # nipype version information # Remove -dev for release -__version__ = '1.3.0-dev' +__version__ = '1.3.0-rc1' def get_nipype_gitversion(): From 215349b9c3a6a9925fbfbf2a7cfd6d01f66964ce Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 7 Oct 2019 16:59:41 -0400 Subject: [PATCH 3/8] CI: Use Python 3.6.5 environment for packaging --- .circleci/config.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index a5d59eb75b..3fc27bf663 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -339,6 +339,7 @@ jobs: - run: name: Check pypi preconditions command: | + pyenv local 3.6.5 pip install --upgrade pip twine future wheel readme_renderer setuptools python setup.py sdist bdist_wheel twine check dist/* @@ -353,7 +354,7 @@ jobs: - run: name: Validate Python 3 installation command: | - pyenv local 3.5.2 + pyenv local 3.6.5 pip install --upgrade pip pip install dist/nipype-*-py2.py3-none-any.whl # Futures should not install in Python 3 @@ -388,6 +389,7 @@ jobs: - run: name: Deploy to PyPI command: | + pyenv local 3.6.5 pip install --upgrade twine future wheel readme_renderer setuptools python setup.py check -r -s python setup.py sdist bdist_wheel From 50952d7483bef049dc565492815ac9fcaeb6fd88 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 8 Oct 2019 07:20:52 -0400 Subject: [PATCH 4/8] MNT: Update mailmap, tracking down ambiguous authors --- .mailmap | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.mailmap b/.mailmap index ced66b4099..edb9ca5a4d 100644 --- a/.mailmap +++ b/.mailmap @@ -70,6 +70,7 @@ Horea Christian Isaac Schwabacher Jakub Kaczmarzyk James Kent +James Kent Fred Mertz Janosch Linkersdörfer Jason Wong Jason Wong @@ -80,6 +81,7 @@ Joerg Stadler Joerg Stadler Joerg Stadler John A. Lee +John A. Lee Joke Durnez Josh Warner Junhao WEN @@ -151,6 +153,7 @@ Shariq Iqbal Shariq Iqbal Shoshana Berleant Shoshana Berleant Shoshana Berleant +Shoshana Berleant Ubuntu Simon Rothmei Simon Rothmei Siqi Liu From a0ee11c452db39fe951ee73d9b7ae1ac03575ed7 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 8 Oct 2019 07:21:51 -0400 Subject: [PATCH 5/8] FIX: Always propagate existing Zenodo authors --- tools/update_zenodo.py | 40 +++++++++++----------------------------- 1 file changed, 11 insertions(+), 29 deletions(-) diff --git a/tools/update_zenodo.py b/tools/update_zenodo.py index c83e14ff14..2833194cd1 100755 --- a/tools/update_zenodo.py +++ b/tools/update_zenodo.py @@ -7,28 +7,8 @@ from fuzzywuzzy import fuzz, process import subprocess as sp -# These ORCIDs should go last +# These names should go last CREATORS_LAST = ['Gorgolewski, Krzysztof J.', 'Ghosh, Satrajit'] -# for entries not found in line-contributions -MISSING_ENTRIES = [ - {"name": "Varada, Jan"}, - {"name": "Schwabacher, Isaac"}, - {"affiliation": "Child Mind Institute / Nathan Kline Institute", - "name": "Pellman, John", - "orcid": "0000-0001-6810-4461"}, - {"name": "Khanuja, Ranjeet"}, - {"affiliation": - "Medical Imaging & Biomarkers, Bioclinica, Newark, CA, USA.", - "name": "Pannetier, Nicolas", - "orcid": "0000-0002-0744-5155"}, - {"name": "McDermottroe, Conor"}, - {"affiliation": - "Max Planck Institute for Human Cognitive and Brain Sciences, " - "Leipzig, Germany.", - "name": "Mihai, Paul Glad", - "orcid": "0000-0001-5715-6442"}, - {"name": "Lai, Jeff"} -] if __name__ == '__main__': contrib_file = Path('line-contributors.txt') @@ -55,7 +35,7 @@ zenodo = json.loads(zenodo_file.read_text()) zen_names = [' '.join(val['name'].split(',')[::-1]).strip() for val in zenodo['creators']] - total_names = len(zen_names) + len(MISSING_ENTRIES) + total_names = len(zen_names) name_matches = [] position = 1 @@ -63,13 +43,14 @@ matches = process.extract(ele, zen_names, scorer=fuzz.token_sort_ratio, limit=2) # matches is a list [('First match', % Match), ('Second match', % Match)] - if matches[0][1] > 80: - val = zenodo['creators'][zen_names.index(matches[0][0])] - else: + if matches[0][1] <= 80: # skip unmatched names print("No entry to sort:", ele) continue + idx = zen_names.index(matches[0][0]) + val = zenodo['creators'][idx] + if val not in name_matches: if val['name'] not in CREATORS_LAST: val['position'] = position @@ -78,10 +59,11 @@ val['position'] = total_names + CREATORS_LAST.index(val['name']) name_matches.append(val) - for missing in MISSING_ENTRIES: - missing['position'] = position - position += 1 - name_matches.append(missing) + for missing in zenodo['creators']: + if 'position' not in missing: + missing['position'] = position + position += 1 + name_matches.append(missing) zenodo['creators'] = sorted(name_matches, key=lambda k: k['position']) # Remove position From 21ef45edb57e03cccdb24c88b97593f4d52be043 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 8 Oct 2019 07:32:37 -0400 Subject: [PATCH 6/8] DOC: Update .zenodo.json ordering --- .zenodo.json | 165 ++++++++++++++++++++++++++------------------------- 1 file changed, 84 insertions(+), 81 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index ac9972984b..d4600474db 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -11,18 +11,13 @@ "orcid": "0000-0002-6533-164X" }, { - "affiliation": "Independent", - "name": "Ziegler, Erik", + "affiliation": "MIT", + "name": "Jarecka, Dorota", "orcid": "0000-0003-1857-8129" }, { - "affiliation": "The University of Iowa", - "name": "Ellis, David Gage", - "orcid": "0000-0002-3718-6836" - }, - { - "affiliation": "MIT", - "name": "Jarecka, Dorota", + "affiliation": "Independent", + "name": "Ziegler, Erik", "orcid": "0000-0003-1857-8129" }, { @@ -30,11 +25,6 @@ "name": "Johnson, Hans", "orcid": "0000-0001-9513-2660" }, - { - "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" - }, { "name": "Burns, Christopher" }, @@ -47,9 +37,19 @@ "name": "Hamalainen, Carlo", "orcid": "0000-0001-7655-3830" }, + { + "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" + }, { "name": "Yvernault, Benjamin" }, + { + "affiliation": "The University of Iowa", + "name": "Ellis, David Gage", + "orcid": "0000-0002-3718-6836" + }, { "affiliation": "Florida International University", "name": "Salo, Taylor", @@ -74,7 +74,8 @@ "name": "Wong, Jason" }, { - "name": "Modat, Marc" + "affiliation": "Concordia University", + "name": "Benderoff, Erin" }, { "affiliation": "Developer", @@ -110,6 +111,9 @@ "affiliation": "National Institutes of Health", "name": "Clark, Michael G. " }, + { + "name": "Modat, Marc" + }, { "affiliation": "Mayo Clinic, Neurology, Rochester, MN, USA", "name": "Dayan, Michael", @@ -138,13 +142,6 @@ "name": "Gramfort, Alexandre", "orcid": "0000-0001-9791-4404" }, - { - "name": "Berleant, Shoshana" - }, - { - "affiliation": "Concordia University", - "name": "Benderoff, Erin" - }, { "affiliation": "Dartmouth College: Hanover, NH, United States", "name": "Halchenko, Yaroslav O.", @@ -155,16 +152,14 @@ "name": "Christian, Horea", "orcid": "0000-0001-7037-2449" }, + { + "name": "Berleant, Shoshana" + }, { "affiliation": "The Centre for Addiction and Mental Health", "name": "Joseph, Michael", "orcid": "0000-0002-0068-230X" }, - { - "affiliation": "UC San Diego", - "name": "Cipollini, Ben", - "orcid": "0000-0002-7782-0790" - }, { "affiliation": "ARAMIS LAB, Brain and Spine Institute (ICM), Paris, France.", "name": "Guillon, Je\u0301re\u0301my", @@ -181,13 +176,13 @@ }, { "affiliation": "Montreal Neurological Institute and Hospital", - "name": "DuPre, Elizabeth", - "orcid": "0000-0003-1358-196X" + "name": "Markello, Ross", + "orcid": "0000-0003-1057-1336" }, { "affiliation": "Montreal Neurological Institute and Hospital", - "name": "Markello, Ross", - "orcid": "0000-0003-1057-1336" + "name": "DuPre, Elizabeth", + "orcid": "0000-0003-1358-196X" }, { "affiliation": "MIT", @@ -197,6 +192,11 @@ { "name": "Moloney, Brendan" }, + { + "affiliation": "UC San Diego", + "name": "Cipollini, Ben", + "orcid": "0000-0002-7782-0790" + }, { "affiliation": "INRIA", "name": "Varoquaux, Gael", @@ -287,9 +287,6 @@ "name": "Bottenhorn, Katherine", "orcid": "0000-0002-7796-8795" }, - { - "name": "Kent, James" - }, { "name": "Watanabe, Aimi" }, @@ -343,6 +340,9 @@ "name": "Liem, Franz", "orcid": "0000-0003-0646-4810" }, + { + "name": "Kent, James" + }, { "affiliation": "UniversityHospital Heidelberg, Germany", "name": "Kleesiek, Jens" @@ -365,11 +365,6 @@ { "name": "Ghayoor, Ali" }, - { - "affiliation": "Otto-von-Guericke-University Magdeburg, Germany", - "name": "Contier, Oliver", - "orcid": "0000-0002-2983-4709" - }, { "name": "K\u00fcttner, Ren\u00e9" }, @@ -379,6 +374,9 @@ { "name": "Millman, Jarrod" }, + { + "name": "Lai, Jeff" + }, { "name": "Zhou, Dale" }, @@ -406,9 +404,9 @@ "orcid": "0000-0002-2127-0507" }, { - "affiliation": "Leibniz Institute for Neurobiology", - "name": "Stadler, J\u00f6rg", - "orcid": "0000-0003-4313-129X" + "affiliation": "Yale University; New Haven, CT, United States", + "name": "Sisk, Lucinda M.", + "orcid": "0000-0003-4900-9770" }, { "affiliation": "Korea Advanced Institute of Science and Technology", @@ -437,16 +435,6 @@ { "name": "Hallquist, Michael" }, - { - "affiliation": "Yale University; New Haven, CT, United States", - "name": "Sisk, Lucinda M.", - "orcid": "0000-0003-4900-9770" - }, - { - "affiliation": "TIB \u2013 Leibniz Information Centre for Science and Technology and University Library, Hannover, Germany", - "name": "Leinweber, Katrin", - "orcid": "0000-0001-5135-5758" - }, { "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging", "name": "Chetverikov, Andrey", @@ -495,9 +483,14 @@ "name": "Hinds, Oliver" }, { - "affiliation": "University of Newcastle, Australia", - "name": "Cooper, Gavin", - "orcid": "0000-0002-7186-5293" + "affiliation": "National Institute on Aging, Baltimore, MD, USA", + "name": "Bilgel, Murat", + "orcid": "0000-0001-5042-7422" + }, + { + "affiliation": "TIB \u2013 Leibniz Information Centre for Science and Technology and University Library, Hannover, Germany", + "name": "Leinweber, Katrin", + "orcid": "0000-0001-5135-5758" }, { "name": "Inati, Souheil" @@ -506,15 +499,6 @@ "affiliation": "Boston University", "name": "Perkins, L. Nathan" }, - { - "name": "Marina, Ana" - }, - { - "name": "Mattfeld, Aaron" - }, - { - "name": "Noel, Maxime" - }, { "affiliation": "University of Amsterdam", "name": "Lukas Snoek", @@ -524,14 +508,30 @@ "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany", "name": "Weninger, Leon" }, + { + "affiliation": "University of Newcastle, Australia", + "name": "Cooper, Gavin", + "orcid": "0000-0002-7186-5293" + }, + { + "name": "Mattfeld, Aaron" + }, { "name": "Matsubara, K" }, + { + "name": "Noel, Maxime" + }, { "affiliation": "University of Pennsylvania", "name": "Junhao WEN", "orcid": "0000-0003-2077-3070" }, + { + "affiliation": "Leibniz Institute for Neurobiology", + "name": "Stadler, J\u00f6rg", + "orcid": "0000-0003-4313-129X" + }, { "name": "Cheung, Brian" }, @@ -563,10 +563,6 @@ "name": "Gerhard, Stephan", "orcid": "0000-0003-4454-6171" }, - { - "affiliation": "University of Illinois Urbana Champaign", - "name": "Sharp, Paul" - }, { "affiliation": "Technical University Munich", "name": "Molina-Romero, Miguel", @@ -578,14 +574,14 @@ { "name": "Weinstein, Alejandro" }, + { + "name": "Tambini, Arielle" + }, { "affiliation": "Duke University", "name": "Broderick, William", "orcid": "0000-0002-8999-9003" }, - { - "name": "Saase, Victor" - }, { "name": "Rothmei, Simon" }, @@ -594,17 +590,9 @@ "name": "Andberg, Sami Kristian", "orcid": "0000-0002-5650-3964" }, - { - "name": "Harms, Robbert" - }, { "name": "Khanuja, Ranjeet" }, - { - "affiliation": "National Institute on Aging, Baltimore, MD, USA", - "name": "Bilgel, Murat", - "orcid": "0000-0001-5042-7422" - }, { "name": "Schlamp, Kai" }, @@ -620,10 +608,11 @@ "name": "Tarbert, Claire" }, { - "name": "Tambini, Arielle" + "name": "Harms, Robbert" }, { - "name": "Nickson, Thomas" + "affiliation": "University of Illinois Urbana Champaign", + "name": "Sharp, Paul" }, { "name": "Crusoe, Michael R.", @@ -676,6 +665,20 @@ { "name": "Davison, Andrew" }, + { + "affiliation": "Otto-von-Guericke-University Magdeburg, Germany", + "name": "Contier, Oliver", + "orcid": "0000-0002-2983-4709" + }, + { + "name": "Marina, Ana" + }, + { + "name": "Saase, Victor" + }, + { + "name": "Nickson, Thomas" + }, { "name": "Varada, Jan" }, From b417e47d101440a2b88dc2d348d45f6b346ec01b Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 8 Oct 2019 07:33:24 -0400 Subject: [PATCH 7/8] DOC: Add Olivia Stanley to Zenodo --- .zenodo.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.zenodo.json b/.zenodo.json index d4600474db..85938865fe 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -538,6 +538,10 @@ { "name": "Urchs, Sebastian" }, + { + "affiliation": "Dept of Medical Biophysics, Univeristy of Western Ontario", + "name": "Stanley, Olivia" + }, { "affiliation": "Department of Psychology, Stanford University; Parietal, INRIA", "name": "Durnez, Joke", From f35d7a7fd4faf0336e1850719a7164cb1b4430ca Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 8 Oct 2019 08:14:25 -0400 Subject: [PATCH 8/8] DOC: Restore Zenodo entries that have been dropped over time --- .zenodo.json | 35 +++++++++++++++++++++++++++++++++-- 1 file changed, 33 insertions(+), 2 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 85938865fe..e65bbe084a 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -369,7 +369,9 @@ "name": "K\u00fcttner, Ren\u00e9" }, { - "name": "Perez-Guevara, Martin" + "affiliation": "Neurospin/Unicog/Inserm/CEA", + "name": "Perez-Guevara, Martin Felipe", + "orcid": "0000-0003-4497-861X" }, { "name": "Millman, Jarrod" @@ -501,7 +503,7 @@ }, { "affiliation": "University of Amsterdam", - "name": "Lukas Snoek", + "name": "Snoek, Lukas", "orcid": "0000-0001-8972-204X" }, { @@ -669,6 +671,35 @@ { "name": "Davison, Andrew" }, + { + "name": "Bielievtsov, Dmytro", + "orcid": "0000-0003-3846-7696" + }, + { + "affiliation": "MPI-CBS; McGill University", + "name": "Steele, Christopher John", + "orcid": "0000-0003-1656-7928" + }, + { + "affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China", + "name": "Huang, Lijie", + "orcid": "0000-0002-9910-5069" + }, + { + "affiliation": "Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA", + "name": "Gonzalez, Ivan", + "orcid": "0000-0002-6451-6909" + }, + { + "affiliation": "Mayo Clinic", + "name": "Warner, Joshua", + "orcid": "0000-0003-3579-4835" + }, + { + "affiliation": "Max Planck Research Group for Neuroanatomy & Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany", + "name": "Margulies, Daniel S.", + "orcid": "0000-0002-8880-9204" + }, { "affiliation": "Otto-von-Guericke-University Magdeburg, Germany", "name": "Contier, Oliver",