Merge branch 'master' into ants_regsynquick

Author: djarecka

.circleci/config.yml

@@ -183,6 +183,28 @@ jobs:
       - run: *_run_codecov_coverage
       - store_artifacts: *store_artifacts_kwds
       - store_test_results: *store_artifacts_kwds
+      - run:
+          name: Build docs (py36)
+          no_output_timeout: 30m
+          environment: *test_environment
+          command: bash -ux /home/circleci/nipype/.circleci/test_py3_docs.sh
+      - store_artifacts:
+          path: /home/circleci/work/docs
+      - run:
+          name: Save Docker images to workspace if on master
+          no_output_timeout: 60m
+          command: |
+            if [ "$CIRCLE_BRANCH" = "master" -a -z "$CIRCLE_PULL_REQUEST" ]; then
+              docker save nipype/nipype:base \
+                          nipype/nipype:latest \
+                          nipype/nipype:py27 \
+                          nipype/nipype:py36 | gzip -1 > /tmp/docker/nipype-base-latest-py36-py27.tar.gz \
+              && du -h /tmp/docker/nipype-base-latest-py36-py27.tar.gz
+            fi
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+            - docker
 
   test_py3_fmri_fsl_spm:
     machine: *machine_kwds
@@ -200,11 +222,6 @@ jobs:
       - run: *_get_codecov
       - run: *_download_test_data
       - run: *prepare_working_directory
-      - run:
-          name: Run FSL FEEDS pipeline (py36)
-          no_output_timeout: 40m
-          environment: *test_environment
-          command: bash -ux /home/circleci/nipype/.circleci/test_py3_fmri_fsl_feeds_linear_l1.sh
       - run:
           name: Run FSL reuse pipeline (py36)
           no_output_timeout: 40m
@@ -252,7 +269,7 @@ jobs:
       - run: *_run_codecov_smoke
       - store_artifacts: *store_artifacts_kwds
 
-  test_fmri_spm_nested_multiproc:
+  test_fmri_spm_nested_fsl_feeds:
     machine: *machine_kwds
     working_directory: /home/circleci/nipype
     steps:
@@ -279,30 +296,13 @@ jobs:
           no_output_timeout: 30m
           environment: *test_environment
           command: bash -ux /home/circleci/nipype/.circleci/test_py2_fmri_spm_nested_multiproc_l2.sh
-      - run: *_run_codecov_smoke
-      - store_artifacts: *store_artifacts_kwds
       - run:
-          name: Build docs (py36)
-          no_output_timeout: 30m
+          name: Run FSL FEEDS pipeline (py36)
+          no_output_timeout: 40m
           environment: *test_environment
-          command: bash -ux /home/circleci/nipype/.circleci/test_py3_docs.sh
-      - store_artifacts:
-          path: /home/circleci/work/docs
-      - run:
-          name: Save Docker images to workspace if on master
-          no_output_timeout: 60m
-          command: |
-            if [ "$CIRCLE_BRANCH" = "master" -a -z "$CIRCLE_PULL_REQUEST" ]; then
-              docker save nipype/nipype:base \
-                          nipype/nipype:latest \
-                          nipype/nipype:py27 \
-                          nipype/nipype:py36 | gzip -1 > /tmp/docker/nipype-base-latest-py36-py27.tar.gz \
-              && du -h /tmp/docker/nipype-base-latest-py36-py27.tar.gz
-            fi
-      - persist_to_workspace:
-          root: /tmp
-          paths:
-            - docker
+          command: bash -ux /home/circleci/nipype/.circleci/test_py3_fmri_fsl_feeds_linear_l1.sh
+      - run: *_run_codecov_smoke
+      - store_artifacts: *store_artifacts_kwds
 
   deploy:
     docker:
@@ -350,7 +350,7 @@ workflows:
       - test_py3_fmri_spm_dartel_multiproc:
           requires:
             - compare_base_dockerfiles
-      - test_fmri_spm_nested_multiproc:
+      - test_fmri_spm_nested_fsl_feeds:
           requires:
             - compare_base_dockerfiles
       - deploy:
@@ -359,6 +359,6 @@ workflows:
               only: master
           requires:
             - test_pytest
-            - test_fmri_spm_nested_multiproc
+            - test_fmri_spm_nested_fsl_feeds
             - test_py3_fmri_fsl_spm
             - test_py3_fmri_spm_dartel_multiproc

.travis.yml

@@ -40,7 +40,7 @@ before_install:
   fi;
 
 # handle python operations separately to reduce timeouts
-- wget https://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
+- wget https://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-4.3.31-Linux-x86_64.sh
     -O /home/travis/.cache/conda.sh
 - bash ${HOME}/.cache/conda.sh -b -p ${HOME}/conda
 - export PATH=${HOME}/conda/bin:$PATH

.zenodo.json

@@ -605,6 +605,10 @@
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729"
+    },
+    {
+      "affiliation": "Vrije Universiteit Amsterdam",
+      "name": "Ort, Eduard"
     }
   ],
   "keywords": [

CHANGES

@@ -1,6 +1,3 @@
-Upcoming release
-================
-
 1.0.0 (January 24, 2018)
 ========================
 

docker/generate_dockerfiles.sh

@@ -88,6 +88,7 @@ function generate_main_dockerfile() {
   --user neuro \
   --miniconda env_name=neuro \
               activate=true \
+              miniconda_version=4.3.31 \
   --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \
          docker/files/run_pytests.sh nipype/external/fsl_imglob.py /usr/bin/ \
   --copy . /src/nipype \

nipype/algorithms/confounds.py

@@ -532,7 +532,7 @@ def _run_interface(self, runtime):
                 # Derive TR from NIfTI header, if possible
                 try:
                     TR = imgseries.header.get_zooms()[3]
-                    if imgseries.get_xyzt_units()[1] == 'msec':
+                    if imgseries.header.get_xyzt_units()[1] == 'msec':
                         TR /= 1000
                 except (AttributeError, IndexError):
                     TR = 0

tools/update_changes.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+#
+# Collects the pull-requests since the latest release and
+# aranges them in the CHANGES.txt file.
+#
+# This is a script to be run before releasing a new version.
+#
+# Usage /bin/bash update_changes.sh 1.0.1
+#
+
+# Setting      # $ help set
+set -u         # Treat unset variables as an error when substituting.
+set -x         # Print command traces before executing command.
+
+# Check whether the Upcoming release header is present
+head -1 CHANGES | grep -q Upcoming
+UPCOMING=$?
+
+# Elaborate today's release header
+HEADER="$1 ($(date '+%B %d, %Y'))"
+echo $HEADER >> newchanges
+echo $( printf "%${#HEADER}s" | tr " " "=" ) >> newchanges
+echo "" >> newchanges
+
+# 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
+
+# Append old CHANGES
+if [[ "$UPCOMING" == "0" ]]; then
+    # Drop the Upcoming title if present
+    tail -n+4 CHANGES >> newchanges
+else
+    cat CHANGES >> newchanges
+fi
+
+# Replace old CHANGES with new file
+mv newchanges CHANGES
+