From 794da9deb706cae913245e5d05ea9684b858efca Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Thu, 8 Sep 2016 11:10:18 -0700
Subject: [PATCH 01/30] replaced coveralls with codecov

---
 .travis.yml | 3 ++-
 circle.yml  | 2 ++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 2c64797512..f677f8f005 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -37,13 +37,14 @@ install:
 - rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*
 - pip install -r requirements.txt
 - pip install -e .
+- pip install codecov
 - export COVERAGE_PROCESS_START=$(pwd)/.coveragerc
 - export COVERAGE_DATA_FILE=$(pwd)/.coverage
 - echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START}
 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}
+- codecov
 deploy:
   provider: pypi
   user: satra
diff --git a/circle.yml b/circle.yml
index 9674e095b5..78e7741dbb 100644
--- a/circle.yml
+++ b/circle.yml
@@ -26,6 +26,7 @@ dependencies:
     - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
         timeout: 1600
     - pip install xunitmerge
+    - pip install codecov
 
 test:
   override:
@@ -50,6 +51,7 @@ test:
 
   post:
     - bash docker/circleci/teardown.sh
+    - codecov
 
 general:
   artifacts:

From fb013480d55604591c63a4bd51462bb147852382 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Thu, 8 Sep 2016 11:14:28 -0700
Subject: [PATCH 02/30] replaced the badge

---
 README.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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

From 78cc31d4e84f3ea62185e222c8eb79ac14cf8052 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Thu, 8 Sep 2016 11:31:51 -0700
Subject: [PATCH 03/30] get coverage from example runs

---
 docker/circleci/run_examples.sh | 5 +++--
 docker/circleci/teardown.sh     | 4 ++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/docker/circleci/run_examples.sh b/docker/circleci/run_examples.sh
index 99d57add58..b6dece9b4c 100644
--- a/docker/circleci/run_examples.sh
+++ b/docker/circleci/run_examples.sh
@@ -11,6 +11,7 @@ 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 $@
+coverate run python /root/src/nipype/tools/run_examples.py $@
+coverage xml -o /scratch/smoketest_${@//[^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..f6019832bc 100644
--- a/docker/circleci/teardown.sh
+++ b/docker/circleci/teardown.sh
@@ -7,10 +7,10 @@ set -u
 set -e
 
 mkdir -p ${CIRCLE_TEST_REPORTS}/nose
-xunitmerge ~/scratch/nosetests*.xml ${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml
+xunitmerge ~/scratch/nosetests*.xml ~/scratch/smoketest*.xml ${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml
 sudo mv ~/scratch/coverage*.xml ~/
 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/

From a6182a937e566388b8b9af802f22c47d6814939b Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Thu, 8 Sep 2016 11:38:37 -0700
Subject: [PATCH 04/30] switch to bash codecov

---
 .travis.yml | 3 +--
 circle.yml  | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index f677f8f005..3711f6da0f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -37,14 +37,13 @@ install:
 - rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*
 - pip install -r requirements.txt
 - pip install -e .
-- pip install codecov
 - export COVERAGE_PROCESS_START=$(pwd)/.coveragerc
 - export COVERAGE_DATA_FILE=$(pwd)/.coverage
 - echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START}
 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:
-- codecov
+- bash <(curl -s https://codecov.io/bash)
 deploy:
   provider: pypi
   user: satra
diff --git a/circle.yml b/circle.yml
index 78e7741dbb..8f04460b4f 100644
--- a/circle.yml
+++ b/circle.yml
@@ -26,7 +26,6 @@ dependencies:
     - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
         timeout: 1600
     - pip install xunitmerge
-    - pip install codecov
 
 test:
   override:
@@ -51,7 +50,7 @@ test:
 
   post:
     - bash docker/circleci/teardown.sh
-    - codecov
+    - bash <(curl -s https://codecov.io/bash)
 
 general:
   artifacts:

From b6763c2c1e64373dc7b5f983e3a1c509b0ed2e5a Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Thu, 8 Sep 2016 13:58:46 -0700
Subject: [PATCH 05/30] fixed a typo

---
 docker/circleci/run_examples.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/circleci/run_examples.sh b/docker/circleci/run_examples.sh
index b6dece9b4c..c4d19a62b3 100644
--- a/docker/circleci/run_examples.sh
+++ b/docker/circleci/run_examples.sh
@@ -11,7 +11,7 @@ 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
 
-coverate run python /root/src/nipype/tools/run_examples.py $@
+coverage run python /root/src/nipype/tools/run_examples.py $@
 coverage xml -o /scratch/smoketest_${@//[^A-Za-z0-9._-]/_}.xml
 
 chmod 777 -R /scratch/logs

From ce23a6d7bfedfadde091a9888e2832709c76be4d Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Thu, 8 Sep 2016 18:59:59 -0700
Subject: [PATCH 06/30] doh

---
 docker/circleci/run_examples.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/circleci/run_examples.sh b/docker/circleci/run_examples.sh
index c4d19a62b3..0b54b8cc36 100644
--- a/docker/circleci/run_examples.sh
+++ b/docker/circleci/run_examples.sh
@@ -11,7 +11,7 @@ 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
 
-coverage run python /root/src/nipype/tools/run_examples.py $@
+coverage run /root/src/nipype/tools/run_examples.py $@
 coverage xml -o /scratch/smoketest_${@//[^A-Za-z0-9._-]/_}.xml
 
 chmod 777 -R /scratch/logs

From 82a2b818f9d65d82d0638761f149e186afbe4cfa Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Thu, 8 Sep 2016 23:03:49 -0700
Subject: [PATCH 07/30] fixed xml paths

---
 docker/circleci/run_examples.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/circleci/run_examples.sh b/docker/circleci/run_examples.sh
index 0b54b8cc36..d9811487b6 100644
--- a/docker/circleci/run_examples.sh
+++ b/docker/circleci/run_examples.sh
@@ -12,6 +12,6 @@ echo 'log_to_file = true' >> /root/.nipype/nipype.cfg
 echo 'log_directory = /scratch/logs/' >> /root/.nipype/nipype.cfg
 
 coverage run /root/src/nipype/tools/run_examples.py $@
-coverage xml -o /scratch/smoketest_${@//[^A-Za-z0-9._-]/_}.xml
+coverage xml -o "/scratch/smoketest_${@//[^A-Za-z0-9._-]/_}.xml"
 
 chmod 777 -R /scratch/logs

From 515a84d8c823adb125d124e549dbe2d5a3f4f675 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 9 Sep 2016 00:35:45 -0700
Subject: [PATCH 08/30] fixed xml paths 2

---
 docker/circleci/run_examples.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/circleci/run_examples.sh b/docker/circleci/run_examples.sh
index d9811487b6..cdb02d8ca8 100644
--- a/docker/circleci/run_examples.sh
+++ b/docker/circleci/run_examples.sh
@@ -12,6 +12,6 @@ echo 'log_to_file = true' >> /root/.nipype/nipype.cfg
 echo 'log_directory = /scratch/logs/' >> /root/.nipype/nipype.cfg
 
 coverage run /root/src/nipype/tools/run_examples.py $@
-coverage xml -o "/scratch/smoketest_${@//[^A-Za-z0-9._-]/_}.xml"
+coverage xml -o "/scratch/smoketest_${@//[^A-Za-z0-9_-]/_}.xml"
 
 chmod 777 -R /scratch/logs

From b2891bebe5783f8b1234978a5654f2b0a9f68f25 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 9 Sep 2016 08:24:06 -0700
Subject: [PATCH 09/30] fixed xml paths 3

---
 docker/circleci/run_examples.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docker/circleci/run_examples.sh b/docker/circleci/run_examples.sh
index cdb02d8ca8..efef7176d9 100644
--- a/docker/circleci/run_examples.sh
+++ b/docker/circleci/run_examples.sh
@@ -12,6 +12,7 @@ echo 'log_to_file = true' >> /root/.nipype/nipype.cfg
 echo 'log_directory = /scratch/logs/' >> /root/.nipype/nipype.cfg
 
 coverage run /root/src/nipype/tools/run_examples.py $@
-coverage xml -o "/scratch/smoketest_${@//[^A-Za-z0-9_-]/_}.xml"
+tmp_var=$( IFS=$' '; echo "${@[*]}" )
+coverage xml -o "/scratch/smoketest_${tmp_var//[^A-Za-z0-9_-]/_}.xml"
 
 chmod 777 -R /scratch/logs

From 5b93067b87a74afc2c73924d018453b142278690 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 9 Sep 2016 09:45:16 -0700
Subject: [PATCH 10/30] fixed xml 4

---
 docker/circleci/run_examples.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docker/circleci/run_examples.sh b/docker/circleci/run_examples.sh
index efef7176d9..5d8697e3e2 100644
--- a/docker/circleci/run_examples.sh
+++ b/docker/circleci/run_examples.sh
@@ -12,7 +12,8 @@ echo 'log_to_file = true' >> /root/.nipype/nipype.cfg
 echo 'log_directory = /scratch/logs/' >> /root/.nipype/nipype.cfg
 
 coverage run /root/src/nipype/tools/run_examples.py $@
-tmp_var=$( IFS=$' '; echo "${@[*]}" )
+arr=$@
+tmp_var=$( IFS=$' '; echo "${arr[*]}" )
 coverage xml -o "/scratch/smoketest_${tmp_var//[^A-Za-z0-9_-]/_}.xml"
 
 chmod 777 -R /scratch/logs

From c500c94d3528aa91b92f72854ad3c8fe23a3aad4 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 9 Sep 2016 15:13:51 -0700
Subject: [PATCH 11/30] explicitly point to a coverage file

---
 circle.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/circle.yml b/circle.yml
index 8f04460b4f..44c4b904d7 100644
--- a/circle.yml
+++ b/circle.yml
@@ -50,7 +50,7 @@ test:
 
   post:
     - bash docker/circleci/teardown.sh
-    - bash <(curl -s https://codecov.io/bash)
+    - bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml
 
 general:
   artifacts:

From a344a258c7132b97a9353ab9358d031e7932907d Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 9 Sep 2016 15:15:08 -0700
Subject: [PATCH 12/30] save scratch

---
 circle.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/circle.yml b/circle.yml
index 44c4b904d7..0053ac0ea9 100644
--- a/circle.yml
+++ b/circle.yml
@@ -7,6 +7,7 @@ dependencies:
     - "~/docker"
     - "~/examples"
     - "~/.apt-cache"
+    - "~/scratch"
 
   pre:
     # Let CircleCI cache the apt archive

From de065445b9443c0eb8baadee779bfae26f48dd65 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 9 Sep 2016 15:23:46 -0700
Subject: [PATCH 13/30] simplify for sake of speed

---
 circle.yml | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/circle.yml b/circle.yml
index 0053ac0ea9..505a0ec3e8 100644
--- a/circle.yml
+++ b/circle.yml
@@ -22,32 +22,32 @@ dependencies:
     - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
     - docker build -f docker/nipype_test/Dockerfile_py35 -t nipype/nipype_test:py35 . :
         timeout: 1600
-    - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
-        timeout: 1600
+    # - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
+    #     timeout: 1600
     - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
         timeout: 1600
     - pip install xunitmerge
 
 test:
   override:
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
+    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
     - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 :
         timeout: 2600
-    - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
-        timeout: 2600
+    # - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
+    #     timeout: 2600
     - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :
         timeout: 1600
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
-        timeout: 1600
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 :
-        timeout: 1600
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
-        timeout: 1600
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
-    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
-    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
-    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
+    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
+    #     timeout: 1600
+    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
+    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 :
+    #     timeout: 1600
+    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
+    #     timeout: 1600
+    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
+    # - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    # - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    # - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
 
   post:
     - bash docker/circleci/teardown.sh

From 72139aeb248388c727bebe56b669f9ef2d8bdeff Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 9 Sep 2016 16:22:27 -0700
Subject: [PATCH 14/30] reanable docs

---
 circle.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/circle.yml b/circle.yml
index 505a0ec3e8..5a45282a0b 100644
--- a/circle.yml
+++ b/circle.yml
@@ -30,7 +30,7 @@ dependencies:
 
 test:
   override:
-    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
     - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 :
         timeout: 2600
     # - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :

From cd4b4b232b8d91ae678b7e6b3ec15a8edc7ceabe Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 9 Sep 2016 18:31:05 -0700
Subject: [PATCH 15/30] add token

---
 circle.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/circle.yml b/circle.yml
index 5a45282a0b..9c2a08a0aa 100644
--- a/circle.yml
+++ b/circle.yml
@@ -51,7 +51,7 @@ test:
 
   post:
     - bash docker/circleci/teardown.sh
-    - bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml
+    - bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml -t ac172a50-8e66-42e5-8822-5373fcf54686
 
 general:
   artifacts:

From a92ee53789bd37247f077c29ab0a174329903fae Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 9 Sep 2016 18:59:39 -0700
Subject: [PATCH 16/30] add flags

---
 .travis.yml | 2 +-
 circle.yml  | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 3711f6da0f..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:
-- bash <(curl -s https://codecov.io/bash)
+- bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
 deploy:
   provider: pypi
   user: satra
diff --git a/circle.yml b/circle.yml
index 9c2a08a0aa..ace498d7d8 100644
--- a/circle.yml
+++ b/circle.yml
@@ -51,7 +51,8 @@ test:
 
   post:
     - bash docker/circleci/teardown.sh
-    - bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml -t ac172a50-8e66-42e5-8822-5373fcf54686
+    - bash <(curl -s https://codecov.io/bash) -f ~/scratch/nosetest*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
+    - bash <(curl -s https://codecov.io/bash) -f ~/scratch/smoketest*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF smoketests
 
 general:
   artifacts:

From bdf79f7411fcb6843949da84c32da2c425b49aa2 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 9 Sep 2016 19:14:28 -0700
Subject: [PATCH 17/30] cache

---
 circle.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/circle.yml b/circle.yml
index ace498d7d8..7eb0295893 100644
--- a/circle.yml
+++ b/circle.yml
@@ -24,8 +24,8 @@ dependencies:
         timeout: 1600
     # - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
     #     timeout: 1600
-    - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
-        timeout: 1600
+    # - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
+    #     timeout: 1600
     - pip install xunitmerge
 
 test:

From a848cc3424ebd925a5187f79c2a8a56a0c14e7bb Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 9 Sep 2016 21:56:32 -0700
Subject: [PATCH 18/30] reenabling other tests

---
 circle.yml | 34 +++++++++++++++++-----------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/circle.yml b/circle.yml
index 7eb0295893..df35dc9c83 100644
--- a/circle.yml
+++ b/circle.yml
@@ -22,10 +22,10 @@ dependencies:
     - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
     - docker build -f docker/nipype_test/Dockerfile_py35 -t nipype/nipype_test:py35 . :
         timeout: 1600
-    # - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
-    #     timeout: 1600
-    # - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
-    #     timeout: 1600
+    - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
+        timeout: 1600
+    - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
+        timeout: 1600
     - pip install xunitmerge
 
 test:
@@ -33,21 +33,21 @@ test:
     - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
     - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 :
         timeout: 2600
-    # - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
-    #     timeout: 2600
+    - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
+        timeout: 2600
     - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :
         timeout: 1600
-    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
-    #     timeout: 1600
-    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
-    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 :
-    #     timeout: 1600
-    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
-    #     timeout: 1600
-    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
-    # - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
-    # - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
-    # - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
+        timeout: 1600
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 :
+        timeout: 1600
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
+        timeout: 1600
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
+    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
 
   post:
     - bash docker/circleci/teardown.sh

From 0a36a2acbfbf6fcc4a9c36bbcca7498c0d4d7f7d Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Sat, 10 Sep 2016 09:39:23 -0700
Subject: [PATCH 19/30] don't cache scratch

---
 circle.yml                  | 5 ++---
 docker/circleci/teardown.sh | 2 +-
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/circle.yml b/circle.yml
index df35dc9c83..79c6b328d1 100644
--- a/circle.yml
+++ b/circle.yml
@@ -7,7 +7,6 @@ dependencies:
     - "~/docker"
     - "~/examples"
     - "~/.apt-cache"
-    - "~/scratch"
 
   pre:
     # Let CircleCI cache the apt archive
@@ -51,8 +50,8 @@ test:
 
   post:
     - bash docker/circleci/teardown.sh
-    - bash <(curl -s https://codecov.io/bash) -f ~/scratch/nosetest*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
-    - bash <(curl -s https://codecov.io/bash) -f ~/scratch/smoketest*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF smoketests
+    - bash <(curl -s https://codecov.io/bash) -f ~/nosetest*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
+    - bash <(curl -s https://codecov.io/bash) -f ~/smoketest*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF smoketests
 
 general:
   artifacts:
diff --git a/docker/circleci/teardown.sh b/docker/circleci/teardown.sh
index f6019832bc..1cc3b9aa70 100644
--- a/docker/circleci/teardown.sh
+++ b/docker/circleci/teardown.sh
@@ -8,7 +8,7 @@ set -e
 
 mkdir -p ${CIRCLE_TEST_REPORTS}/nose
 xunitmerge ~/scratch/nosetests*.xml ~/scratch/smoketest*.xml ${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml
-sudo mv ~/scratch/coverage*.xml ~/
+sudo mv ~/scratch/*.xml ~/
 mkdir -p ~/docs
 sudo mv ~/scratch/docs/* ~/docs/
 mkdir -p ~/logs

From 7cae63bee80c078f57d43bcc71894db0f33e12cc Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Sat, 10 Sep 2016 10:18:39 -0700
Subject: [PATCH 20/30] simplify things

---
 circle.yml                  | 10 ++--------
 docker/circleci/teardown.sh |  3 +--
 2 files changed, 3 insertions(+), 10 deletions(-)

diff --git a/circle.yml b/circle.yml
index 79c6b328d1..a410632076 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:
@@ -50,15 +49,10 @@ test:
 
   post:
     - bash docker/circleci/teardown.sh
-    - bash <(curl -s https://codecov.io/bash) -f ~/nosetest*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
-    - bash <(curl -s https://codecov.io/bash) -f ~/smoketest*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF smoketests
+    - bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/coverage*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
+    - bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/smoketest*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests
 
 general:
   artifacts:
     - "~/docs"
     - "~/logs"
-    - "~/coverage_py27.xml"
-    - "~/coverage_py35.xml"
-    - "~/nosetests_py27.xml"
-    - "~/nosetests_py35.xml"
-    - "~/scratch"
diff --git a/docker/circleci/teardown.sh b/docker/circleci/teardown.sh
index 1cc3b9aa70..c7ef852f5c 100644
--- a/docker/circleci/teardown.sh
+++ b/docker/circleci/teardown.sh
@@ -7,8 +7,7 @@ set -u
 set -e
 
 mkdir -p ${CIRCLE_TEST_REPORTS}/nose
-xunitmerge ~/scratch/nosetests*.xml ~/scratch/smoketest*.xml ${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml
-sudo mv ~/scratch/*.xml ~/
+sudo mv ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/nose
 mkdir -p ~/docs
 sudo mv ~/scratch/docs/* ~/docs/
 mkdir -p ~/logs

From 5993af556b46c28648c1c3aaf0a4fc70e77b6536 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Sat, 10 Sep 2016 16:12:55 -0700
Subject: [PATCH 21/30] fixed codecov pattern

---
 circle.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/circle.yml b/circle.yml
index a410632076..2f1f89ed45 100644
--- a/circle.yml
+++ b/circle.yml
@@ -49,8 +49,8 @@ test:
 
   post:
     - bash docker/circleci/teardown.sh
-    - bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/coverage*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
-    - bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/smoketest*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests
+    - bash <(curl -s https://codecov.io/bash) -f "${CIRCLE_TEST_REPORTS}/nose/coverage*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
+    - bash <(curl -s https://codecov.io/bash) -f "${CIRCLE_TEST_REPORTS}/nose/smoketest*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests
 
 general:
   artifacts:

From 6a169ed7bf316979db0607d96164a70ac6b98591 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Sat, 10 Sep 2016 16:17:08 -0700
Subject: [PATCH 22/30] adde codecov.yml

---
 codecov.yml | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 codecov.yml

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/"

From e6c82bca8f2067ad7089bb350ae6ca6d65c72989 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Sat, 10 Sep 2016 22:12:33 -0700
Subject: [PATCH 23/30] asteriks cleanup

---
 circle.yml                  | 4 ++--
 docker/circleci/teardown.sh | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/circle.yml b/circle.yml
index 2f1f89ed45..9c4ba456b5 100644
--- a/circle.yml
+++ b/circle.yml
@@ -49,8 +49,8 @@ test:
 
   post:
     - bash docker/circleci/teardown.sh
-    - bash <(curl -s https://codecov.io/bash) -f "${CIRCLE_TEST_REPORTS}/nose/coverage*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
-    - bash <(curl -s https://codecov.io/bash) -f "${CIRCLE_TEST_REPORTS}/nose/smoketest*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests
+    - bash <(curl -s https://codecov.io/bash) -f "/home/ubuntu/scratch/coverage*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
+    - bash <(curl -s https://codecov.io/bash) -f "/home/ubuntu/scratch/smoketest*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests
 
 general:
   artifacts:
diff --git a/docker/circleci/teardown.sh b/docker/circleci/teardown.sh
index c7ef852f5c..823192632d 100644
--- a/docker/circleci/teardown.sh
+++ b/docker/circleci/teardown.sh
@@ -7,7 +7,7 @@ set -u
 set -e
 
 mkdir -p ${CIRCLE_TEST_REPORTS}/nose
-sudo mv ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/nose
+sudo cp ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/nose
 mkdir -p ~/docs
 sudo mv ~/scratch/docs/* ~/docs/
 mkdir -p ~/logs

From 7d8125db11e09d0fc2bb4556c59cdb73d573e6d3 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Sun, 11 Sep 2016 10:37:01 -0700
Subject: [PATCH 24/30] submit reports from withing docker containers

---
 circle.yml                       | 42 +++++++++++++++++---------------
 docker/circleci/run_nosetests.sh |  3 +++
 2 files changed, 25 insertions(+), 20 deletions(-)

diff --git a/circle.yml b/circle.yml
index 9c4ba456b5..b6f3bcf590 100644
--- a/circle.yml
+++ b/circle.yml
@@ -21,36 +21,38 @@ dependencies:
     - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
     - docker build -f docker/nipype_test/Dockerfile_py35 -t nipype/nipype_test:py35 . :
         timeout: 1600
-    - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
-        timeout: 1600
+    # - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
+    #     timeout: 1600
     - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
         timeout: 1600
 
 test:
   override:
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
+    - docker run $ci_env -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
     - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 :
         timeout: 2600
-    - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
-        timeout: 2600
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :
-        timeout: 1600
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
-        timeout: 1600
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 :
-        timeout: 1600
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
-        timeout: 1600
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
-    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
-    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
-    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
+        environment:
+          - ci_env: `bash <(curl -s https://codecov.io/env)`
+    # - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
+    #     timeout: 2600
+    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :
+    #     timeout: 1600
+    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
+    #     timeout: 1600
+    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
+    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 :
+    #     timeout: 1600
+    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
+    #     timeout: 1600
+    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
+    # - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    # - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    # - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
 
   post:
     - bash docker/circleci/teardown.sh
-    - bash <(curl -s https://codecov.io/bash) -f "/home/ubuntu/scratch/coverage*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
-    - bash <(curl -s https://codecov.io/bash) -f "/home/ubuntu/scratch/smoketest*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests
+    # - bash <(curl -s https://codecov.io/bash) -f "/home/ubuntu/scratch/coverage*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
+    # - bash <(curl -s https://codecov.io/bash) -f "/home/ubuntu/scratch/smoketest*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests
 
 general:
   artifacts:
diff --git a/docker/circleci/run_nosetests.sh b/docker/circleci/run_nosetests.sh
index 9e912e20de..d0258eef5c 100644
--- a/docker/circleci/run_nosetests.sh
+++ b/docker/circleci/run_nosetests.sh
@@ -24,13 +24,16 @@ fi
 cd /root/src/nipype/
 make clean
 nosetests -s nipype -c /root/src/nipype/.noserc --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}.xml"
+bash <(curl -s https://codecov.io/bash) -f /scratch/coverage_py${PYTHON_VERSION}.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
 
 # Workaround: run here the profiler tests in python 3
 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
     echo '[execution]' >> /root/.nipype/nipype.cfg
     echo 'profile_runtime = true' >> /root/.nipype/nipype.cfg
     nosetests nipype/interfaces/tests/test_runtime_profiler.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_profiler.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_profiler.xml"
+    bash <(curl -s https://codecov.io/bash) -f /scratch/coverage_py${PYTHON_VERSION}_profiler.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
     nosetests nipype/pipeline/plugins/tests/test_multiproc*.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_multiproc.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_multiproc.xml"
+    bash <(curl -s https://codecov.io/bash) -f /scratch/coverage_py${PYTHON_VERSION}_multiproc.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
 fi
 
 # Copy crashfiles to scratch

From 1f622266ce4847b735440f39dc8309645280a121 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Sun, 11 Sep 2016 10:41:56 -0700
Subject: [PATCH 25/30] submit reports from withing docker containers 2

---
 circle.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/circle.yml b/circle.yml
index b6f3bcf590..78d5b95721 100644
--- a/circle.yml
+++ b/circle.yml
@@ -28,11 +28,9 @@ dependencies:
 
 test:
   override:
-    - docker run $ci_env -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
-    - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 :
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
+    - export ci_env=`bash <(curl -s https://codecov.io/env)` && docker run $ci_env -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 :
         timeout: 2600
-        environment:
-          - ci_env: `bash <(curl -s https://codecov.io/env)`
     # - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
     #     timeout: 2600
     # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :

From c54de25ce3cf33d68978aec45eb1ce43faa60909 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Sun, 11 Sep 2016 11:08:56 -0700
Subject: [PATCH 26/30] strip

---
 circle.yml                  | 8 ++++----
 docker/circleci/teardown.sh | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/circle.yml b/circle.yml
index 78d5b95721..9569da54d0 100644
--- a/circle.yml
+++ b/circle.yml
@@ -23,12 +23,12 @@ dependencies:
         timeout: 1600
     # - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
     #     timeout: 1600
-    - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
-        timeout: 1600
+    # - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
+    #     timeout: 1600
 
 test:
   override:
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
+    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
     - export ci_env=`bash <(curl -s https://codecov.io/env)` && docker run $ci_env -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 :
         timeout: 2600
     # - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
@@ -54,5 +54,5 @@ test:
 
 general:
   artifacts:
-    - "~/docs"
+    # - "~/docs"
     - "~/logs"
diff --git a/docker/circleci/teardown.sh b/docker/circleci/teardown.sh
index 823192632d..aba1140e6d 100644
--- a/docker/circleci/teardown.sh
+++ b/docker/circleci/teardown.sh
@@ -8,8 +8,8 @@ set -e
 
 mkdir -p ${CIRCLE_TEST_REPORTS}/nose
 sudo cp ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/nose
-mkdir -p ~/docs
-sudo mv ~/scratch/docs/* ~/docs/
+# mkdir -p ~/docs
+# sudo mv ~/scratch/docs/* ~/docs/
 mkdir -p ~/logs
 sudo mv ~/scratch/builddocs.log ~/logs/builddocs.log
 sudo mv ~/scratch/logs/* ~/logs/

From 341db5a0e95d32082d85c80295d734ca6a3445a8 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Sun, 11 Sep 2016 13:08:35 -0700
Subject: [PATCH 27/30] more debug

---
 docker/circleci/run_nosetests.sh | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/docker/circleci/run_nosetests.sh b/docker/circleci/run_nosetests.sh
index d0258eef5c..f69b57d162 100644
--- a/docker/circleci/run_nosetests.sh
+++ b/docker/circleci/run_nosetests.sh
@@ -3,6 +3,8 @@ set -e
 set -x
 set -u
 
+env
+
 PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" )
 
 # Create necessary directories
@@ -24,16 +26,16 @@ fi
 cd /root/src/nipype/
 make clean
 nosetests -s nipype -c /root/src/nipype/.noserc --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}.xml"
-bash <(curl -s https://codecov.io/bash) -f /scratch/coverage_py${PYTHON_VERSION}.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
+bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
 
 # Workaround: run here the profiler tests in python 3
 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
     echo '[execution]' >> /root/.nipype/nipype.cfg
     echo 'profile_runtime = true' >> /root/.nipype/nipype.cfg
     nosetests nipype/interfaces/tests/test_runtime_profiler.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_profiler.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_profiler.xml"
-    bash <(curl -s https://codecov.io/bash) -f /scratch/coverage_py${PYTHON_VERSION}_profiler.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
+    bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
     nosetests nipype/pipeline/plugins/tests/test_multiproc*.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_multiproc.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_multiproc.xml"
-    bash <(curl -s https://codecov.io/bash) -f /scratch/coverage_py${PYTHON_VERSION}_multiproc.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
+    bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
 fi
 
 # Copy crashfiles to scratch

From 2637541de9e1c134c60137e5238517ffaade23e5 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Sun, 11 Sep 2016 13:21:19 -0700
Subject: [PATCH 28/30] reverting

---
 circle.yml                       | 48 ++++++++++++++++----------------
 docker/circleci/run_nosetests.sh |  5 ----
 docker/circleci/teardown.sh      |  6 ++--
 tools/run_examples.py            |  3 +-
 4 files changed, 28 insertions(+), 34 deletions(-)

diff --git a/circle.yml b/circle.yml
index 9569da54d0..a410632076 100644
--- a/circle.yml
+++ b/circle.yml
@@ -21,38 +21,38 @@ dependencies:
     - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
     - docker build -f docker/nipype_test/Dockerfile_py35 -t nipype/nipype_test:py35 . :
         timeout: 1600
-    # - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
-    #     timeout: 1600
-    # - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
-    #     timeout: 1600
+    - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
+        timeout: 1600
+    - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
+        timeout: 1600
 
 test:
   override:
-    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
-    - export ci_env=`bash <(curl -s https://codecov.io/env)` && docker run $ci_env -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 :
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
+    - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 :
         timeout: 2600
-    # - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
-    #     timeout: 2600
-    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :
-    #     timeout: 1600
-    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
-    #     timeout: 1600
-    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
-    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 :
-    #     timeout: 1600
-    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
-    #     timeout: 1600
-    # - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
-    # - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
-    # - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
-    # - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
+    - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
+        timeout: 2600
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :
+        timeout: 1600
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
+        timeout: 1600
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 :
+        timeout: 1600
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
+        timeout: 1600
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
+    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
 
   post:
     - bash docker/circleci/teardown.sh
-    # - bash <(curl -s https://codecov.io/bash) -f "/home/ubuntu/scratch/coverage*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
-    # - bash <(curl -s https://codecov.io/bash) -f "/home/ubuntu/scratch/smoketest*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests
+    - bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/coverage*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
+    - bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/smoketest*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests
 
 general:
   artifacts:
-    # - "~/docs"
+    - "~/docs"
     - "~/logs"
diff --git a/docker/circleci/run_nosetests.sh b/docker/circleci/run_nosetests.sh
index f69b57d162..9e912e20de 100644
--- a/docker/circleci/run_nosetests.sh
+++ b/docker/circleci/run_nosetests.sh
@@ -3,8 +3,6 @@ set -e
 set -x
 set -u
 
-env
-
 PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" )
 
 # Create necessary directories
@@ -26,16 +24,13 @@ fi
 cd /root/src/nipype/
 make clean
 nosetests -s nipype -c /root/src/nipype/.noserc --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}.xml"
-bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
 
 # Workaround: run here the profiler tests in python 3
 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
     echo '[execution]' >> /root/.nipype/nipype.cfg
     echo 'profile_runtime = true' >> /root/.nipype/nipype.cfg
     nosetests nipype/interfaces/tests/test_runtime_profiler.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_profiler.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_profiler.xml"
-    bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
     nosetests nipype/pipeline/plugins/tests/test_multiproc*.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_multiproc.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_multiproc.xml"
-    bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
 fi
 
 # Copy crashfiles to scratch
diff --git a/docker/circleci/teardown.sh b/docker/circleci/teardown.sh
index aba1140e6d..c7ef852f5c 100644
--- a/docker/circleci/teardown.sh
+++ b/docker/circleci/teardown.sh
@@ -7,9 +7,9 @@ set -u
 set -e
 
 mkdir -p ${CIRCLE_TEST_REPORTS}/nose
-sudo cp ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/nose
-# mkdir -p ~/docs
-# sudo mv ~/scratch/docs/* ~/docs/
+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/
diff --git a/tools/run_examples.py b/tools/run_examples.py
index 45f4c8dc4f..c34085a8e7 100644
--- a/tools/run_examples.py
+++ b/tools/run_examples.py
@@ -37,8 +37,7 @@ def run_examples(example, pipelines, data_path, plugin=None, rm_base_dir=True):
             os.makedirs(log_dir)
         wf.config = {'execution': {'hash_method': 'timestamp',
                                    'stop_on_first_rerun': 'true',
-                                   'write_provenance': 'true',
-                                   'poll_sleep_duration': 2},
+                                   'write_provenance': 'true'},
                      'logging': {'log_directory': log_dir, 'log_to_file': True}}
         try:
             wf.inputs.inputnode.in_data = os.path.abspath(data_path)

From a08f6ac99ad8062a2579af824233b55cdea00ef0 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Sun, 11 Sep 2016 13:30:00 -0700
Subject: [PATCH 29/30] iterate over xmls explicitly

---
 circle.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/circle.yml b/circle.yml
index a410632076..947d23b694 100644
--- a/circle.yml
+++ b/circle.yml
@@ -49,8 +49,8 @@ test:
 
   post:
     - bash docker/circleci/teardown.sh
-    - bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/coverage*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
-    - bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/smoketest*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests
+    - 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:

From c2ce806420ef92e1e12291c1fef16ba35484dfe6 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Sun, 11 Sep 2016 18:33:45 -0700
Subject: [PATCH 30/30] reverted accidental change

---
 tools/run_examples.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tools/run_examples.py b/tools/run_examples.py
index c34085a8e7..45f4c8dc4f 100644
--- a/tools/run_examples.py
+++ b/tools/run_examples.py
@@ -37,7 +37,8 @@ def run_examples(example, pipelines, data_path, plugin=None, rm_base_dir=True):
             os.makedirs(log_dir)
         wf.config = {'execution': {'hash_method': 'timestamp',
                                    'stop_on_first_rerun': 'true',
-                                   'write_provenance': 'true'},
+                                   'write_provenance': 'true',
+                                   'poll_sleep_duration': 2},
                      'logging': {'log_directory': log_dir, 'log_to_file': True}}
         try:
             wf.inputs.inputnode.in_data = os.path.abspath(data_path)