Merge branch 'nipy:master' into master

Author: bbfrederick

.circleci/config.yml

@@ -1,5 +1,5 @@
 _machine_kwds: &machine_kwds
-  image: circleci/classic:201808-01
+  image: ubuntu-2004:202107-02
 
 _store_artifacts_kwds: &store_artifacts_kwds
   path: /home/circleci/work/tests
@@ -43,15 +43,15 @@ _get_base_image: &get_base_image
       exit 1
     fi
 
-_build_main_image_py36: &build_main_image_py36
-  name: Build main image (py36)
+_build_main_image_py38: &build_main_image_py38
+  name: Build main image (py38)
   no_output_timeout: 60m
   command: |
     tools/retry_cmd.sh -n 5 -s 15 \
       docker build \
         --rm=false \
         --tag nipype/nipype:latest \
-        --tag nipype/nipype:py36 \
+        --tag nipype/nipype:py38 \
         $(test -z "${CIRCLE_TAG}" || echo --tag nipype/nipype:"${CIRCLE_TAG}") \
         --build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
         --build-arg VCS_REF="$(git rev-parse --short HEAD)" \
@@ -146,7 +146,7 @@ jobs:
       - run: *generate_dockerfiles
       - run: *modify_nipype_version
       - run: *get_base_image
-      - run: *build_main_image_py36
+      - run: *build_main_image_py38
       - run: *_get_codecov
       - run: *_download_test_data
       - run: *prepare_working_directory
@@ -165,8 +165,8 @@ jobs:
             if [ "$CIRCLE_BRANCH" = "master" -a -z "$CIRCLE_PULL_REQUEST" ]; then
               docker save nipype/nipype:base \
                           nipype/nipype:latest \
-                          nipype/nipype:py36 | gzip -1 > /tmp/docker/nipype-base-latest-py36.tar.gz \
-              && du -h /tmp/docker/nipype-base-latest-py36.tar.gz
+                          nipype/nipype:py38 | gzip -1 > /tmp/docker/nipype-base-latest-py38.tar.gz \
+              && du -h /tmp/docker/nipype-base-latest-py38.tar.gz
             fi
       - persist_to_workspace:
           root: /tmp
@@ -184,15 +184,15 @@ jobs:
           name: Load saved Docker images.
           no_output_timeout: 60m
           command: |
-            docker load < /tmp/docker/nipype-base-latest-py36.tar.gz
+            docker load < /tmp/docker/nipype-base-latest-py38.tar.gz
       - run:
           name: Push to DockerHub
           no_output_timeout: 120m
           command: |
             echo "$DOCKER_PASS" | docker login -u "$DOCKER_USER" --password-stdin
             docker push nipype/nipype:base
             docker push nipype/nipype:latest
-            docker push nipype/nipype:py36
+            docker push nipype/nipype:py38
             test -z "${CIRCLE_TAG}" || docker push nipype/nipype:"${CIRCLE_TAG}"
       - run:
           name: Move pruned Dockerfile to /tmp/docker/cache directory

.circleci/test_pytest.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py36" /usr/bin/run_pytests.sh
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py38" /usr/bin/run_pytests.sh

.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"
@@ -313,6 +318,11 @@
       "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"
     },
@@ -726,6 +736,11 @@
       "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 +809,19 @@
       "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"
     },

README.rst

@@ -82,7 +82,7 @@ Python 2 Statement
 
 Python 2.7 reaches its end-of-life in January 2020, which means it will
 *no longer be maintained* by Python developers. `Many projects
-<https://python3statement.org/`__ are removing support in advance of this
+<https://python3statement.org/>`__ are removing support in advance of this
 deadline, which will make it increasingly untenable to try to support
 Python 2, even if we wanted to.
 

doc/_static/nipype.css

@@ -5,6 +5,10 @@ body {
     min-width: 70em;
 }
 
+div.sphinxsidebar {
+    position: relative;
+}
+
 div.sphinxsidebar h4, div.sphinxsidebar h3 {
     background-color: #2F83C8;
 }

doc/_templates/layout.html

@@ -2,6 +2,9 @@
 {% set title = 'Neuroimaging in Python - Pipelines and Interfaces' %}
 {% set short_title = 'Nipype' %}
 
+{% block sidebar1 %}{{ sidebar() }}{% endblock %}
+{% block sidebar2 %}{% endblock %}
+
 {% block extrahead %}
 {{ super() }}
 <meta name="keywords" content="nipype, neuroimaging, pipeline, workflow, parallel, python, neuroscience">
@@ -42,8 +45,6 @@
 
 {% block relbar1 %}{% endblock %}
 {% block relbar2 %}{% endblock %}
-{% block sidebar1 %}{{ sidebar() }}{% endblock %}
-{% block sidebar2 %}{% endblock %}
 
 {% block footer %}
 {{ super() }}

doc/_templates/navbar.html

@@ -1,7 +1,6 @@
 <link rel="stylesheet" href="https://www.google.com/cse/style/look/default.css" type="text/css" />
 <style type="text/css">
     a.navbar {
-    color: {{ theme_linkcolor }};
     letter-spacing: .05em;
     font-weight: bold;
         }

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/conf.py

@@ -152,7 +152,7 @@
 
 # General information about the project.
 project = u"nipype"
-copyright = u"2009-20, Neuroimaging in Python team"
+copyright = u"2009-21, Neuroimaging in Python team"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/devel/testing_nipype.rst

@@ -90,16 +90,15 @@ Testing Nipype using Docker
 Nipype is tested inside Docker containers and users can use nipype images to test local versions.
 First, install the `Docker Engine <https://docs.docker.com/engine/installation/>`_.
 Nipype has one base docker image called nipype/nipype:base, that contains several useful tools
-(FreeSurfer, AFNI, FSL, ANTs, etc.), and additional test images
-for specific Python versions: py27 for Python 2.7 and py36 for Python 3.6.
+(FreeSurfer, AFNI, FSL, ANTs, etc.), and an additional test image for Python 3.8:
 
-Users can pull the nipype image for Python 3.6 as follows::
+Users can pull the nipype image for Python 3.8 as follows::
 
-  docker pull nipype/nipype:py36
+  docker pull nipype/nipype:py38
 
 In order to test a local version of nipype you can run test within container as follows::
 
-  docker run -it -v $PWD:/src/nipype --rm nipype/nipype:py36 py.test -v --doctest-modules /src/nipype/nipype
+  docker run -it -v $PWD:/src/nipype --rm nipype/nipype:py38 py.test -v --doctest-modules /src/nipype/nipype
 
 
 Additional comments

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: `1.7.0 <http://nipype.readthedocs.io/en/1.7.0/>`_ `1.6.1 <http://nipype.readthedocs.io/en/1.6.1/>`_
 
 Workflows
 ---------

docker/generate_dockerfiles.sh

@@ -89,6 +89,8 @@ function generate_main_dockerfile() {
           OMP_NUM_THREADS=1 \
     --arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=8 BUILD_DATE VCS_REF VERSION \
     --user neuro \
+    --run 'git config --global user.name nipybot
+           && git config --global user.email "nipybot@gmail.com"' \
     --workdir /home/neuro \
     --miniconda create_env=neuro \
                 conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}