Merge pull request #3446 from nipy/rel/1.7.1

REL: 1.7.1
nipy · Apr 5, 2022 · f8f7fb5 · f8f7fb5
2 parents 4ac2189 + b7c3df0
commit f8f7fb5
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Showing 7 changed files with 97 additions and 58 deletions.
diff --git 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 "[email protected]"
+            git config --global hub.protocol ssh
       - run:
           name: Update feedstock
           command: |

diff --git a/.mailmap b/.mailmap
@@ -11,6 +11,7 @@ Alexander Schaefer <[email protected]> <aschaefer@aschaefer-U36SD.(none)>
 Alexandre M. Savio <[email protected]>
 Alexandre M. Savio <[email protected]> <[email protected]>
 Andrea Dell'Orco <[email protected]>
+Andrea Dell'Orco <[email protected]> <[email protected]>
 Andrew Floren <[email protected]>
 Andrey Chetverikov <[email protected]>
 Andrey Chetverikov <[email protected]> <[email protected]>
@@ -64,6 +65,8 @@ Elizabeth DuPre <[email protected]>
 Erik Ziegler <[email protected]>
 Erik Ziegler <[email protected]> <[email protected]>
 Erik Ziegler <[email protected]> <erik@erik-ubuntu.(none)>
+Fabio Bernardoni <[email protected]>
+Fabio Bernardoni <[email protected]> <[email protected]>
 Feilong Ma <[email protected]>
 Fernando Pérez-García <[email protected]>
 Franz Liem <[email protected]>
@@ -109,6 +112,7 @@ Kevin Sitek <[email protected]>
 Kevin Sitek <[email protected]> <[email protected]>
 Sin Kim <[email protected]>
 Sin Kim <[email protected]> <[email protected]>
+Koen Helwegen <[email protected]>
 Kornelius Podranski <[email protected]>
 Krzysztof J. Gorgolewski <[email protected]>
 Krzysztof J. Gorgolewski <[email protected]> <[email protected]>
@@ -121,6 +125,7 @@ Kshitij Chawla <[email protected]>
 Leonie Lampe <[email protected]>
 Lukas Snoek <[email protected]>
 Marcel Falkiewicz <[email protected]> <[email protected]>
+Maria de Fatima Dias <[email protected]>
 Maria de Fatima Dias <[email protected]> <[email protected]>
 Martin Perez-Guevara <[email protected]>
 Mathias Goncalves <[email protected]> <[email protected]>
@@ -153,6 +158,8 @@ Oscar Esteban <[email protected]>
 Oscar Esteban <[email protected]> <code@oscaresteban>
 Pablo Polosecki <[email protected]> <[email protected]>
 Pablo Polosecki <[email protected]> <[email protected]>
+Paul Kuntke <[email protected]>
+Paul Kuntke <[email protected]> <[email protected]>
 Paul Sharp <[email protected]>
 Ranjit Khanuja <[email protected]>
 Rastko Ćirić <[email protected]>

diff --git 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",

diff --git 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 <https://github.com/nipy/nipype/milestone/1.7.1?closed=1>`__)
+
+  * 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)
 ========================
 

diff --git 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'],
 
 

diff --git 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():

diff --git 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}
@@ -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
@@ -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~" \
@@ -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 - <<END
+    hub pull-request -b conda-forge:main -F - <<END
 $PR_TITLE
 
 Updating feedstock to release branch