Merge pull request #3392 from nipy/rel/1.7.0

REL: 1.7.0

.mailmap

@@ -10,6 +10,7 @@ Alexander Schaefer <alexschaefer83@gmail.com> <aschaefer@melisse.cbs.mpg.de>
 Alexander Schaefer <alexschaefer83@gmail.com> <aschaefer@aschaefer-U36SD.(none)>
 Alexandre M. Savio <alexsavio@gmail.com>
 Alexandre M. Savio <alexsavio@gmail.com> <alexsavio@users.noreply.github.com>
+Andrea Dell'Orco <orco@paranoici.org>
 Andrew Floren <andrewfloren@gmail.com>
 Andrey Chetverikov <stop.psy@gmail.com>
 Andrey Chetverikov <stop.psy@gmail.com> <achetverikov@users.noreply.github.com>
@@ -144,6 +145,7 @@ Michael Waskom <michael.l.waskom@gmail.com> <mwaskom@stanford.edu>
 Miguel Molina-Romero <miguel.molina.romero@gmail.com>
 Murat Bilgel <bilgelm@gmail.com> <murat.bilgel@nih.gov>
 Nat Lee <vip3268@gmail.com>
+Ole Numssen <numssen@cbs.mpg.de>
 Oliver Contier <o.contier@gmail.com> <oliver.contier@ovgu.de>
 Olivia Stanley <oliviawstanley@gmail.com>
 Oscar Esteban <code@oscaresteban.es>

.zenodo.json

@@ -148,15 +148,15 @@
       "name": "Visconti di Oleggio Castello, Matteo",
       "orcid": "0000-0001-7931-5272"
     },
-    {
-      "affiliation": "Shattuck Lab, UCLA Brain Mapping Center",
-      "name": "Wong, Jason"
-    },
     {
       "affiliation": "University of Texas at Austin",
       "name": "De La Vega, Alejandro",
       "orcid": "0000-0001-9062-3778"
     },
+    {
+      "affiliation": "Shattuck Lab, UCLA Brain Mapping Center",
+      "name": "Wong, Jason"
+    },
     {
       "affiliation": "MIT",
       "name": "Kaczmarzyk, Jakub",
@@ -217,6 +217,11 @@
       "name": "de Hollander, Gilles",
       "orcid": "0000-0003-1988-5091"
     },
+    {
+      "affiliation": "Charit\u00e8 Universit\u00e4tsmedizin Berlin, Germany",
+      "name": "Dell'Orco, Andrea",
+      "orcid": "0000-0002-3964-8360"
+    },
     {
       "affiliation": "University College London",
       "name": "Eshaghi, Arman",
@@ -251,6 +256,11 @@
     {
       "name": "Mordom, David"
     },
+    {
+      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
+      "name": "Waller, Lea",
+      "orcid": "0000-0002-3239-6957"
+    },
     {
       "affiliation": "CIBIT, UC",
       "name": "Machado, F\u00e1tima",
@@ -261,11 +271,6 @@
       "name": "Guillon, Je\u0301re\u0301my",
       "orcid": "0000-0002-2672-7510"
     },
-    {
-      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
-      "name": "Waller, Lea",
-      "orcid": "0000-0002-3239-6957"
-    },
     {
       "affiliation": "Indiana University, IN, USA",
       "name": "Koudoro, Serge"
@@ -726,6 +731,11 @@
       "affiliation": "Universidad de Guadalajara",
       "name": "Gonz\u00e1lez Orozco, Abel A."
     },
+    {
+      "affiliation": "ARAMIS Lab",
+      "name": "Routier, Alexandre",
+      "orcid": "0000-0003-1603-8049"
+    },
     {
       "name": "Marina, Ana"
     },
@@ -794,9 +804,19 @@
       "name": "Pannetier, Nicolas",
       "orcid": "0000-0002-0744-5155"
     },
+    {
+      "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences",
+      "name": "Numssen, Ole",
+      "orcid": "0000-0001-7164-2682"
+    },
     {
       "name": "Khanuja, Ranjeet"
     },
+    {
+      "affiliation": "University of Waterloo",
+      "name": "Mukhometzianov, Rinat",
+      "orcid": "0000-0003-1274-4827"
+    },
     {
       "name": "Urchs, Sebastian"
     },
@@ -835,11 +855,6 @@
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729"
-    },
-    {
-      "affiliation": "Charitè Universitätsmedizin Berlin, Germany",
-      "name": "Dell\'Orco, Andrea",
-      "orcid": "0000-0002-3964-8360"
     }
   ],
   "keywords": [

doc/changelog/1.X.X-changelog.rst

@@ -1,3 +1,26 @@
+1.7.0 (October 20, 2021)
+========================
+
+(`Full changelog <https://github.com/nipy/nipype/milestone/1.7.0?closed=1>`__)
+
+  * FIX: Make ants.LaplacianThickness output_image a string, not file (https://github.com/nipy/nipype/pull/3393)
+  * FIX: coord for mrconvert (https://github.com/nipy/nipype/pull/3369)
+  * FIX: ``antsRegistration`` allows the ``restrict_deformation`` to be float  (https://github.com/nipy/nipype/pull/3387)
+  * FIX: Also allow `errno.EBUSY` during `emptydirs` on NFS  (https://github.com/nipy/nipype/pull/3357)
+  * FIX: Removed exists=True from MathsOutput (https://github.com/nipy/nipype/pull/3385)
+  * FIX: Extension not extensions, after pybids v0.9 (https://github.com/nipy/nipype/pull/3380)
+  * ENH: Add CAT12 SANLM denoising filter (https://github.com/nipy/nipype/pull/3374)
+  * ENH: Add expected steps for FreeSurfer 7 recon-all  (https://github.com/nipy/nipype/pull/3389)
+  * ENH: Stop printing false positive differences when logging cached nodes  (https://github.com/nipy/nipype/pull/3376)
+  * ENH: Add new flags to MRtrix/preprocess.py (DWI2Tensor, MRtransform)  (https://github.com/nipy/nipype/pull/3365)
+  * ENH: ``verbose`` input should not be hashed in ``ants.Registration`` (https://github.com/nipy/nipype/pull/3377)
+  * REF: Clean-up the BaseInterface ``run()`` function using context (https://github.com/nipy/nipype/pull/3347)
+  * DOC: Fix typo in README  (https://github.com/nipy/nipype/pull/3386)
+  * STY: Make private member name consistent with the rest of them (https://github.com/nipy/nipype/pull/3346)
+  * MNT: Simplify interface execution and better error handling of ``Node`` (https://github.com/nipy/nipype/pull/3349)
+  * MNT: Add user name and email to Docker to appease git/annex/datalad (https://github.com/nipy/nipype/pull/3378)
+  * CI: Update CircleCI machine image  (https://github.com/nipy/nipype/pull/3391)
+
 1.6.1 (June 16, 2021)
 =====================
 

doc/interfaces.rst

@@ -8,7 +8,7 @@ Interfaces and Workflows
 :Release: |version|
 :Date: |today|
 
-Previous versions: `1.6.0 <http://nipype.readthedocs.io/en/1.6.0/>`_ `1.5.1 <http://nipype.readthedocs.io/en/1.5.1/>`_
+Previous versions: `1.6.1 <http://nipype.readthedocs.io/en/1.6.1/>`_ `1.6.0 <http://nipype.readthedocs.io/en/1.6.0/>`_
 
 Workflows
 ---------

nipype/info.py

@@ -5,7 +5,7 @@
 
 # nipype version information
 # Remove -dev for release
-__version__ = "1.6.1"
+__version__ = "1.7.0"
 
 
 def get_nipype_gitversion():

tools/update_changes.sh

@@ -23,15 +23,30 @@ UPCOMING=$?
 HEADER="$1 ($(date '+%B %d, %Y'))"
 echo $HEADER >> newchanges
 echo $( printf "%${#HEADER}s" | tr " " "=" ) >> newchanges
+echo >> newchanges
 
 if [[ "x$2" != "x" ]]; then
-	echo "(\`Full changelog <https://github.com/nipy/nipype/milestone/$2?closed=1>\`__)" >> newchanges
+    echo "(\`Full changelog <https://github.com/nipy/nipype/milestone/$2?closed=1>\`__)" >> newchanges
+    echo >> newchanges
 fi
 
 # Search for PRs since previous release
-git log --grep="Merge pull request" `git describe --tags --abbrev=0`..HEAD --pretty='format:  * %b %s' | sed  's+Merge pull request \#\([^\d]*\)\ from\ .*+(https://github.com/nipy/nipype/pull/\1)+' >> newchanges
-echo "" >> newchanges
-echo "" >> newchanges
+MERGE_COMMITS=$( git log --grep="Merge pull request\|(#.*)$" `git describe --tags --abbrev=0`..HEAD --pretty='format:%h' )
+for COMMIT in ${MERGE_COMMITS//\n}; do
+    SUB=$( git log -n 1 --pretty="format:%s" $COMMIT )
+    if ( echo $SUB | grep "^Merge pull request" ); then
+        # Merge commit
+        PR=$( echo $SUB | sed -e "s/Merge pull request \#\([0-9]*\).*/\1/" )
+        TITLE=$( git log -n 1 --pretty="format:%b" $COMMIT )
+    else
+        # Squashed merge
+        PR=$( echo $SUB | sed -e "s/.*(\#\([0-9]*\))$/\1/" )
+        TITLE=$( echo $SUB | sed -e "s/\(.*\)(\#[0-9]*)$/\1/" )
+    fi
+    echo "  * $TITLE (https://github.com/nipy/nipype/pull/$PR)" >> newchanges
+done
+echo >> newchanges
+echo >> newchanges
 
 # Append old CHANGES
 if [[ "$UPCOMING" == "0" ]]; then
@@ -43,4 +58,3 @@ fi
 
 # Replace old CHANGES with new file
 mv newchanges $CHANGES
-