From d91d1d55e948dbc0e8a06acc59a7892026075630 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Sun, 3 Apr 2022 12:26:13 -0400 Subject: [PATCH 1/7] DOC: 1.7.1 changelog --- doc/changelog/1.X.X-changelog.rst | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/doc/changelog/1.X.X-changelog.rst b/doc/changelog/1.X.X-changelog.rst index 1bf81b42ab..4e656441b0 100644 --- a/doc/changelog/1.X.X-changelog.rst +++ b/doc/changelog/1.X.X-changelog.rst @@ -1,3 +1,29 @@ +1.7.1 (April 05, 2022) +====================== + +(`Full changelog `__) + + * FIX: Allow ``ConvertScalarImageToRGBInputSpec.mask_file`` to be ``"none"`` (https://github.com/nipy/nipype/pull/3364) + * FIX: Use a more robust strategy for detecting ANTs version (https://github.com/nipy/nipype/pull/3444) + * FIX: Retry renaming pkl(z) files on failure (https://github.com/nipy/nipype/pull/3404) + * FIX: Escape metacharacters when parsing dcm2niix outputs (https://github.com/nipy/nipype/pull/3417) + * FIX: Import error for nipype.interfaces.dipy.base (https://github.com/nipy/nipype/pull/3414) + * FIX: ``ValueError`` when using ``ResourceMonitor`` (https://github.com/nipy/nipype/pull/3419) + * FIX: Improve error handling of ``CommandLine`` interfaces (https://github.com/nipy/nipype/pull/3395) + * FIX: Bugs in ApplyVDM interface (https://github.com/nipy/nipype/pull/3396) + * ENH: Add MRTrix3 interfaces (pared-down gh-3426) (https://github.com/nipy/nipype/pull/3445) + * ENH: Enable BidsDataGrabber to load saved layouts (https://github.com/nipy/nipype/pull/3421) + * ENH: ROBEX interface (https://github.com/nipy/nipype/pull/3443) + * ENH: Include several operations to ANTs's ImageMath interface, including ReplicateImage and ReplicateDisplacement (https://github.com/nipy/nipype/pull/3435) + * ENH: Add "GenericLabel" to antsRegistration interpolation option. (https://github.com/nipy/nipype/pull/3424) + * ENH: added Apply VDM functionality to FieldMap SPM interface (https://github.com/nipy/nipype/pull/3394) + * DOC: Side bar and main page fixes (https://github.com/nipy/nipype/pull/3397) + * TEST: Allow SVD columns to flip sign (https://github.com/nipy/nipype/pull/3405) + * MNT: rename dipy ``move_streamlines`` to ``transform_tracking_output`` (https://github.com/nipy/nipype/pull/3412) + * MNT: Test on Python 3.10 (https://github.com/nipy/nipype/pull/3438) + * MNT: Added ORCID iD (https://github.com/nipy/nipype/pull/3436) + + 1.7.0 (October 20, 2021) ======================== From 7ea309f1625fdbc67aadd18d734413def7b0bd64 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Sun, 3 Apr 2022 12:35:34 -0400 Subject: [PATCH 2/7] MNT: Update mailmap, reorder Zenodo --- .mailmap | 7 ++++ .zenodo.json | 91 ++++++++++++++++++++++++++-------------------------- 2 files changed, 52 insertions(+), 46 deletions(-) diff --git a/.mailmap b/.mailmap index 99dc087a60..e512a6f025 100644 --- a/.mailmap +++ b/.mailmap @@ -11,6 +11,7 @@ Alexander Schaefer Alexandre M. Savio Alexandre M. Savio Andrea Dell'Orco +Andrea Dell'Orco Andrew Floren Andrey Chetverikov Andrey Chetverikov @@ -64,6 +65,8 @@ Elizabeth DuPre Erik Ziegler Erik Ziegler Erik Ziegler +Fabio Bernardoni +Fabio Bernardoni Feilong Ma Fernando Pérez-García Franz Liem @@ -109,6 +112,7 @@ Kevin Sitek Kevin Sitek Sin Kim Sin Kim +Koen Helwegen Kornelius Podranski Krzysztof J. Gorgolewski Krzysztof J. Gorgolewski @@ -121,6 +125,7 @@ Kshitij Chawla Leonie Lampe Lukas Snoek Marcel Falkiewicz +Maria de Fatima Dias Maria de Fatima Dias Martin Perez-Guevara Mathias Goncalves @@ -153,6 +158,8 @@ Oscar Esteban Oscar Esteban Pablo Polosecki Pablo Polosecki +Paul Kuntke +Paul Kuntke Paul Sharp Ranjit Khanuja Rastko Ćirić diff --git a/.zenodo.json b/.zenodo.json index 1f85a8c38b..b04e08cbfb 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -178,6 +178,11 @@ { "name": "Erickson, Drew" }, + { + "affiliation": "CIBIT, UC", + "name": "Dias, Maria de Fatima", + "orcid": "0000-0001-8878-1750" + }, { "affiliation": "Neuroscience Program, University of Iowa", "name": "Kent, James D.", @@ -203,6 +208,11 @@ { "name": "Tungaraza, Rosalia" }, + { + "affiliation": "Charit\u00e8 Universit\u00e4tsmedizin Berlin, Germany", + "name": "Dell'Orco, Andrea", + "orcid": "0000-0002-3964-8360" + }, { "affiliation": "Child Mind Institute", "name": "Frohlich, Caroline" @@ -218,9 +228,8 @@ "orcid": "0000-0003-1988-5091" }, { - "affiliation": "Charit\u00e8 Universit\u00e4tsmedizin Berlin, Germany", - "name": "Dell'Orco, Andrea", - "orcid": "0000-0002-3964-8360" + "affiliation": "Indiana University, IN, USA", + "name": "Koudoro, Serge" }, { "affiliation": "University College London", @@ -250,31 +259,22 @@ "name": "Varoquaux, Gael", "orcid": "0000-0003-1076-5122" }, - { - "name": "Watanabe, Aimi" - }, - { - "name": "Mordom, David" - }, { "affiliation": "Charite Universitatsmedizin Berlin, Germany", "name": "Waller, Lea", "orcid": "0000-0002-3239-6957" }, { - "affiliation": "CIBIT, UC", - "name": "Dias, Maria de Fatima", - "orcid": "0000-0001-8878-1750" + "name": "Watanabe, Aimi" + }, + { + "name": "Mordom, David" }, { "affiliation": "ARAMIS LAB, Brain and Spine Institute (ICM), Paris, France.", "name": "Guillon, Je\u0301re\u0301my", "orcid": "0000-0002-2672-7510" }, - { - "affiliation": "Indiana University, IN, USA", - "name": "Koudoro, Serge" - }, { "affiliation": "Penn Statistics in Imaging and Visualization Endeavor, University of Pennsylvania", "name": "Robert-Fitzgerald, Timothy", @@ -308,6 +308,11 @@ "name": "Gillman, Ashley", "orcid": "0000-0001-9130-1092" }, + { + "affiliation": "Division of Psychological and Social Medicine and Developmental Neuroscience, Faculty of Medicine, Technische Universit\u00e4t Dresden, Dresden, Germany", + "name": "Bernardoni, Fabio", + "orcid": "0000-0002-5112-405X" + }, { "affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China; Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands", "name": "Kong, Xiang-Zhen", @@ -318,11 +323,6 @@ "name": "Geisler, Daniel", "orcid": "0000-0003-2076-5329" }, - { - "affiliation": "Division of Psychological and Social Medicine and Developmental Neuroscience, Faculty of Medicine, Technische Universit\u00e4t Dresden, Dresden, Germany", - "name": "Bernardoni, Fabio", - "orcid": "0000-0002-5112-405X" - }, { "name": "Salvatore, John" }, @@ -416,6 +416,11 @@ "name": "Glatard, Tristan", "orcid": "0000-0003-2620-5883" }, + { + "affiliation": "Sagol School of Neuroscience, Tel Aviv University", + "name": "Baratz, Zvi", + "orcid": "0000-0001-7159-1387" + }, { "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.", "name": "Tabas, Alejandro", @@ -437,11 +442,6 @@ "name": "Iqbal, Shariq", "orcid": "0000-0003-2766-8425" }, - { - "affiliation": "Sagol School of Neuroscience, Tel Aviv University", - "name": "Baratz, Zvi", - "orcid": "0000-0001-7159-1387" - }, { "affiliation": "University of Iowa", "name": "Welch, David" @@ -547,6 +547,9 @@ "name": "Stojic, Hrvoje", "orcid": "0000-0002-9699-9052" }, + { + "name": "Hui Qian, Tan" + }, { "affiliation": "German Institute for International Educational Research", "name": "Linkersd\u00f6rfer, Janosch", @@ -570,6 +573,11 @@ "name": "Pauli, Wolfgang M.", "orcid": "0000-0002-0966-0254" }, + { + "affiliation": "Weill Cornell Medicine", + "name": "Xie, Xihe", + "orcid": "0000-0001-6595-2473" + }, { "affiliation": "NIMH, Scientific and Statistical Computing Core", "name": "Glen, Daniel", @@ -644,6 +652,11 @@ "name": "Lee, Nat", "orcid": "0000-0001-9308-9988" }, + { + "affiliation": "Insitiute and Polyclinc for Diagnostic and Interventional Neuroradiology, University Hospital Carl Gustav Carus, Dresden, Germany", + "name": "Kuntke, Paul", + "orcid": "0000-0003-1838-2230" + }, { "name": "Jalan, Raunak" }, @@ -722,6 +735,11 @@ { "name": "Modat, Marc" }, + { + "affiliation": "University of Waterloo", + "name": "Mukhometzianov, Rinat", + "orcid": "0000-0003-1274-4827" + }, { "name": "Harms, Robbert" }, @@ -818,11 +836,6 @@ { "name": "Khanuja, Ranjeet" }, - { - "affiliation": "University of Waterloo", - "name": "Mukhometzianov, Rinat", - "orcid": "0000-0003-1274-4827" - }, { "name": "Urchs, Sebastian" }, @@ -839,11 +852,6 @@ "name": "Broderick, William", "orcid": "0000-0002-8999-9003" }, - { - "affiliation": "Weill Cornell Medicine", - "name": "Xie, Xihe", - "orcid": "0000-0001-6595-2473" - }, { "name": "Tambini, Arielle" }, @@ -861,16 +869,7 @@ "affiliation": "MIT, HMS", "name": "Ghosh, Satrajit", "orcid": "0000-0002-5312-6729" - }, - { - "name": "Hui Qian, Tan" - }, - { - "affiliation": "Insitiute and Polyclinc for Diagnostic and Interventional Neuroradiology, University Hospital Carl Gustav Carus, Dresden, Germany", - "name": "Kuntke, Paul", - "orcid": "0000-0003-1838-2230" - } - + } ], "keywords": [ "neuroimaging", From cbf75f4ab3271a8099733ff85cb044f7e13d9e78 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Sun, 3 Apr 2022 12:39:20 -0400 Subject: [PATCH 3/7] MNT: Update version to 1.7.1 --- nipype/info.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/info.py b/nipype/info.py index a12eca0ea7..d3df0a3c6f 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -5,7 +5,7 @@ # nipype version information # Remove -dev for release -__version__ = "1.7.1-dev" +__version__ = "1.7.1" def get_nipype_gitversion(): From c722da13e1d789cf13fe06159bf858e5dd694ad9 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Sun, 3 Apr 2022 12:53:10 -0400 Subject: [PATCH 4/7] MNT: conda-forge changed master to main --- tools/feedstock.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/feedstock.sh b/tools/feedstock.sh index b37dba8671..10c8e4cb14 100755 --- a/tools/feedstock.sh +++ b/tools/feedstock.sh @@ -62,7 +62,7 @@ if git checkout -t $GITHUB_USER/$BRANCH; then NEW_PR=false else NEW_PR=true - git checkout -b $BRANCH origin/master + git checkout -b $BRANCH origin/main fi # Calculate hash @@ -90,7 +90,7 @@ git commit -m "$COMMIT_MSG" git push -u $GITHUB_USER $BRANCH if $NEW_PR; then - hub pull-request -b conda-forge:master -F - < Date: Sun, 3 Apr 2022 13:00:07 -0400 Subject: [PATCH 5/7] CI: Upgrade hub, use ssh by default --- .circleci/config.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 0afcb62533..4f1558d6d7 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -213,9 +213,9 @@ jobs: - run: name: Install hub command: | - curl -sSL https://github.com/github/hub/releases/download/v2.2.9/hub-linux-amd64-2.2.9.tgz | \ + curl -sSL https://github.com/github/hub/releases/download/v2.14.2/hub-linux-amd64-2.14.2.tgz | \ tar zxv -C /tmp - sudo /tmp/hub-linux-amd64-2.2.9/install + sudo /tmp/hub-linux-amd64-2.14.2/install - run: name: Expand SSH Key command: | @@ -225,10 +225,11 @@ jobs: chmod go-rwx ~/.ssh/id_ed25519 ssh-keygen -y -f ~/.ssh/id_ed25519 > ~/.ssh/id_ed25519.pub - run: - name: Set git identity + name: Set git/hub configuration command: | git config --global user.name "nipybot" git config --global user.email "nipybot@gmail.com" + git config --global hub.protocol ssh - run: name: Update feedstock command: | From 61bf9ac09aba3bfb2bac6d33dc7dd8dfe7bf8292 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Sun, 3 Apr 2022 13:00:23 -0400 Subject: [PATCH 6/7] ENH: feedstock script should fail on error Update sed command to not raise inconsequential error code --- tools/feedstock.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/feedstock.sh b/tools/feedstock.sh index 10c8e4cb14..0ca82d1751 100755 --- a/tools/feedstock.sh +++ b/tools/feedstock.sh @@ -25,7 +25,7 @@ # # 2018 Chris Markiewicz -set -x +set -ex REPO=${1:-$CIRCLE_PROJECT_REPONAME} FEEDSTOCK=${2:-$REPO-feedstock} @@ -77,7 +77,7 @@ fi # Set version, hash, and reset build number # Use ~ for separator in URL, to avoid slash issues -sed -i '' \ +sed -i \ -e 's/^\({% set version = "\).*\(" %}\)$/'"\1$VERSION\2/" \ -e 's/^\({% set sha256 = "\).*\(" %}\)$/'"\1$SHA256\2/" \ -e 's~^\( *url:\) .*$~\1 '"$URL_FMT~" \ From b7c3df05ae63b569cd0c93814f5cea96e3e94095 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 4 Apr 2022 12:34:06 -0400 Subject: [PATCH 7/7] DOC: Update extras in installation instructions --- doc/users/install.rst | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/doc/users/install.rst b/doc/users/install.rst index 1e55e22907..cbf18c862c 100644 --- a/doc/users/install.rst +++ b/doc/users/install.rst @@ -50,11 +50,17 @@ use the following command:: While `all` installs everything, one can also install select components as listed below:: - 'doc': ['Sphinx>=1.4', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'], - 'tests': ['pytest-cov', 'codecov'], - 'nipy': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'], - 'profiler': ['psutil'], + 'data': ['datalad'], + 'doc': ['dipy', 'ipython', 'matplotlib', 'nbsphinx', 'sphinx-argparse', + 'sphinx>=2.1.2', 'sphinxcontrib-apidoc'], 'duecredit': ['duecredit'], + 'nipy': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'], + 'profiler': ['psutil>=5.0'], + 'pybids': ['pybids>=0.7.0'], + 'specs': ['black'], + 'ssh': ['paramiko'], + 'tests': ['codecov', 'coverage<5', 'pytest', 'pytest-cov', 'pytest-env', + 'pytest-timeout'], 'xvfbwrapper': ['xvfbwrapper'],