merged with new changes

Author: Shoshana Berleant

.travis.yml

@@ -31,7 +31,7 @@ install:
 - conda update --all -y python=$TRAVIS_PYTHON_VERSION
 # - if [[ "${INSTALL_DEB_DEPENDECIES}" == "true" && ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]]; then
 #   conda install -y vtk mayavi; fi
-- conda install -y nipype
+- conda install -y nipype matplotlib nitime
 - pip install python-coveralls coverage doctest-ignore-unicode
 - if [ ! -z "$DUECREDIT_ENABLE"]; then pip install duecredit; fi
 - rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*
@@ -43,7 +43,7 @@ install:
 script:
 - python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-doctest-ignore-unicode --with-cov --cover-package nipype --logging-level=DEBUG --verbosity=3
 after_success:
-- coveralls --config_file ${COVERAGE_PROCESS_START}
+- bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
 deploy:
   provider: pypi
   user: satra

CHANGES

@@ -1,6 +1,7 @@
 Upcoming release 0.13
 =====================
 
+* ENH: Add a DVARS calculation interface (https://github.com/nipy/nipype/pull/1606)
 * ENH: Convenient load/save of interface inputs (https://github.com/nipy/nipype/pull/1591)
 * ENH: Add a Framewise Displacement calculation interface (https://github.com/nipy/nipype/pull/1604)
 * FIX: Use builtins open and unicode literals for py3 compatibility (https://github.com/nipy/nipype/pull/1572)

README.rst

@@ -8,8 +8,8 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
 .. image:: https://circleci.com/gh/nipy/nipype/tree/master.svg?style=svg
   :target: https://circleci.com/gh/nipy/nipype/tree/master
 
-.. image:: https://coveralls.io/repos/nipy/nipype/badge.png
-  :target: https://coveralls.io/r/nipy/nipype
+.. image:: https://codecov.io/gh/nipy/nipype/branch/master/graph/badge.svg
+  :target: https://codecov.io/gh/nipy/nipype
 
 .. image:: https://www.codacy.com/project/badge/182f27944c51474490b369d0a23e2f32
   :target: https://www.codacy.com/app/krzysztof-gorgolewski/nipy_nipype

circle.yml

@@ -25,7 +25,6 @@ dependencies:
         timeout: 1600
     - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
         timeout: 1600
-    - pip install xunitmerge
 
 test:
   override:
@@ -50,13 +49,10 @@ test:
 
   post:
     - bash docker/circleci/teardown.sh
+    - for xml_f in ${CIRCLE_TEST_REPORTS}/nose/coverage*.xml; do bash <(curl -s https://codecov.io/bash) -f $xml_f -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests; done
+    - for xml_f in ${CIRCLE_TEST_REPORTS}/nose/smoketest*.xml; do bash <(curl -s https://codecov.io/bash) -f $xml_f -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests; done
 
 general:
   artifacts:
     - "~/docs"
     - "~/logs"
-    - "~/coverage_py27.xml"
-    - "~/coverage_py35.xml"
-    - "~/nosetests_py27.xml"
-    - "~/nosetests_py35.xml"
-    - "~/scratch"

codecov.yml

@@ -0,0 +1,20 @@
+coverage:
+  range: "0...100"
+  status:
+    project:
+      default:
+        target: 0
+        threshold: 100
+      patch:
+        target: 0
+        threshold: 100
+      unittests:
+        target: 0
+        threshold: 100
+        flags:
+          - "unittests"
+      smoketests:
+        target: 0
+        threshold: 100
+        flags:
+          - "smoketests"

docker/circleci/run_examples.sh

@@ -11,6 +11,9 @@ echo 'filemanip_level = DEBUG' >> /root/.nipype/nipype.cfg
 echo 'log_to_file = true' >> /root/.nipype/nipype.cfg
 echo 'log_directory = /scratch/logs/' >> /root/.nipype/nipype.cfg
 
-python /root/src/nipype/tools/run_examples.py $@
+coverage run /root/src/nipype/tools/run_examples.py $@
+arr=$@
+tmp_var=$( IFS=$' '; echo "${arr[*]}" )
+coverage xml -o "/scratch/smoketest_${tmp_var//[^A-Za-z0-9_-]/_}.xml"
 
-chmod 777 -R /scratch/logs
+chmod 777 -R /scratch/logs

docker/circleci/teardown.sh

@@ -7,10 +7,9 @@ set -u
 set -e
 
 mkdir -p ${CIRCLE_TEST_REPORTS}/nose
-xunitmerge ~/scratch/nosetests*.xml ${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml
-sudo mv ~/scratch/coverage*.xml ~/
+sudo mv ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/nose
 mkdir -p ~/docs
 sudo mv ~/scratch/docs/* ~/docs/
 mkdir -p ~/logs
 sudo mv ~/scratch/builddocs.log ~/logs/builddocs.log
-sudo mv ~/scratch/logs/* ~/logs/
+sudo mv ~/scratch/logs/* ~/logs/

examples/smri_ants_registration.py

@@ -24,6 +24,7 @@
 import urllib.error
 import urllib.parse
 from nipype.interfaces.ants import Registration
+from nipype.testing import example_data
 
 """
 2. Download T1 volumes into home directory
@@ -61,11 +62,12 @@
 
 """
 3. Define the parameters of the registration. Settings are
-saved in ``smri_ants_registration_settings.json``.
+found in the file ``smri_ants_registration_settings.json``
+distributed with the ``example_data`` of `nipype`.
 
 """
 
-reg = Registration(from_file='./smri_ants_registration_settings.json')
+reg = Registration(from_file=example_data('smri_ants_registration_settings.json'))
 reg.inputs.fixed_image = input_images[0]
 reg.inputs.moving_image = input_images[1]