Merge remote-tracking branch 'origin/master' into ENH/nipypeconfdir

Author: stilley2

.circleci/config.yml

@@ -339,6 +339,7 @@ jobs:
       - run:
           name: Check pypi preconditions
           command: |
+            pyenv local 3.6.5
             pip install --upgrade pip twine future wheel readme_renderer setuptools
             python setup.py sdist bdist_wheel
             twine check dist/*
@@ -353,7 +354,7 @@ jobs:
       - run:
           name: Validate Python 3 installation
           command: |
-            pyenv local 3.5.2
+            pyenv local 3.6.5
             pip install --upgrade pip
             pip install dist/nipype-*-py2.py3-none-any.whl
             # Futures should not install in Python 3
@@ -388,6 +389,7 @@ jobs:
       - run:
           name: Deploy to PyPI
           command: |
+            pyenv local 3.6.5
             pip install --upgrade twine future wheel readme_renderer setuptools
             python setup.py check -r -s
             python setup.py sdist bdist_wheel

.et

@@ -0,0 +1,3 @@
+{ "bad_versions" : [ "1.2.1",
+                     "1.2.3"]
+}

.mailmap

@@ -70,6 +70,7 @@ Horea Christian <[email protected]> <[email protected]>
 Isaac Schwabacher <[email protected]>
 Jakub Kaczmarzyk <[email protected]>
 James Kent <[email protected]>
+James Kent <[email protected]> Fred Mertz <[email protected]>
 Janosch Linkersdörfer <[email protected]>
 Jason Wong <[email protected]>
 Jason Wong <[email protected]> <[email protected]>
@@ -80,6 +81,7 @@ Joerg Stadler <[email protected]> <[email protected]>
 Joerg Stadler <[email protected]> <[email protected]>
 Joerg Stadler <[email protected]> <[email protected]>
 John A. Lee <[email protected]>
+John A. Lee <[email protected]> <[email protected]>
 Joke Durnez <[email protected]>
 Josh Warner <[email protected]> <[email protected]>
 Junhao WEN <[email protected]>
@@ -151,6 +153,7 @@ Shariq Iqbal <[email protected]>
 Shariq Iqbal <[email protected]> <[email protected]>
 Shoshana Berleant <[email protected]> Shoshana Berleant <nope>
 Shoshana Berleant <[email protected]> <[email protected]>
+Shoshana Berleant <[email protected]> Ubuntu <[email protected]>
 Simon Rothmei <[email protected]>
 Simon Rothmei <[email protected]> <[email protected]>
 Siqi Liu <[email protected]>

.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.0.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 19.3b0
+    hooks:
+    -   id: black

.travis.yml

@@ -16,6 +16,7 @@ env:
     - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
     - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
     - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
+    - CHECK_TYPE=test
   matrix:
     - INSTALL_DEB_DEPENDECIES=true
       NIPYPE_EXTRAS="doc,tests,nipy,profiler"
@@ -31,35 +32,12 @@ env:
       EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
       CI_SKIP_TEST=1
 
-# Python 3.4 is only available on Trusty, so we need to duplicate the
-# env matrix specifically for it.
 matrix:
   include:
-    - python: 3.4
-      dist: trusty
+    - python: 3.7
       env:
-        - INSTALL_DEB_DEPENDECIES=true
-          NIPYPE_EXTRAS="doc,tests,nipy,profiler"
-          CI_SKIP_TEST=1
-    - python: 3.4
-      dist: trusty
-      env:
-        - INSTALL_DEB_DEPENDECIES=false
-          NIPYPE_EXTRAS="doc,tests,profiler"
-          CI_SKIP_TEST=1
-    - python: 3.4
-      dist: trusty
-      env:
-        - INSTALL_DEB_DEPENDECIES=true
-          NIPYPE_EXTRAS="doc,tests,nipy,profiler,duecredit,ssh"
-          CI_SKIP_TEST=1
-    - python: 3.4
-      dist: trusty
-      env:
-        - INSTALL_DEB_DEPENDECIES=true
-          NIPYPE_EXTRAS="doc,tests,nipy,profiler"
-          EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
-          CI_SKIP_TEST=1
+        - NIPYPE_EXTRAS=dev
+          CHECK_TYPE=specs
 
 addons:
   apt:
@@ -94,7 +72,16 @@ install:
 - travis_retry pip install pytest-xdist
 
 script:
-- py.test -v --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype -n auto
+- |
+    if [ "$CHECK_TYPE" = "test" ]; then
+        py.test -v --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype -n auto
+    fi
+- |
+    if [ "$CHECK_TYPE" = "specs" ]; then
+        make specs
+        git add nipype
+        test "$( git diff --cached | wc -l )" -eq 0 || ( git diff --cached && false )
+    fi
 
 after_script:
 - codecov --file cov.xml --flags unittests -e TRAVIS_JOB_NUMBER