diff --git a/.travis.yml b/.travis.yml
index 2c64797512..fb1e8f3faf 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -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
diff --git a/README.rst b/README.rst
index e1c27aa83a..7e0bd68488 100644
--- a/README.rst
+++ b/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
diff --git a/circle.yml b/circle.yml
index 9674e095b5..947d23b694 100644
--- a/circle.yml
+++ b/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"
diff --git a/codecov.yml b/codecov.yml
new file mode 100644
index 0000000000..6c5d3bb45e
--- /dev/null
+++ b/codecov.yml
@@ -0,0 +1,9 @@
+coverage:
+  status:
+    project:
+      unittests:  # declare a new status context "tests"
+        flags:
+          - "unittests"  # only include coverage in "tests/" folder
+      smoketests:  # declare a new status context "app"
+        paths:
+          - "smoketests"  # remove all files in "tests/"
diff --git a/docker/circleci/run_examples.sh b/docker/circleci/run_examples.sh
index 99d57add58..5d8697e3e2 100644
--- a/docker/circleci/run_examples.sh
+++ b/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
\ No newline at end of file
+chmod 777 -R /scratch/logs
diff --git a/docker/circleci/teardown.sh b/docker/circleci/teardown.sh
index ac14460a3c..c7ef852f5c 100644
--- a/docker/circleci/teardown.sh
+++ b/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/
\ No newline at end of file
+sudo mv ~/scratch/logs/* ~/logs/