From 2a811d48e57ed6add0502d27f1f4d3dcb8be9823 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Mar 2017 09:01:56 -0700
Subject: [PATCH 01/11] protect replacement of imglob with __main__

---
 .noserc                       | 11 -----
 nipype/external/fsl_imglob.py | 93 ++++++++++++++++++-----------------
 2 files changed, 49 insertions(+), 55 deletions(-)
 delete mode 100644 .noserc

diff --git a/.noserc b/.noserc
deleted file mode 100644
index d8c30da437..0000000000
--- a/.noserc
+++ /dev/null
@@ -1,11 +0,0 @@
-[nosetests]
-verbosity=3
-logging-level=DEBUG
-with-doctest=1
-with-doctest-ignore-unicode=1
-
-with-xunit=1
-with-coverage=1
-cover-branches=1
-cover-xml=1
-cover-min-percentage=50
diff --git a/nipype/external/fsl_imglob.py b/nipype/external/fsl_imglob.py
index ca15f70108..f77041c575 100755
--- a/nipype/external/fsl_imglob.py
+++ b/nipype/external/fsl_imglob.py
@@ -65,15 +65,8 @@
 #   innovation@isis.ox.ac.uk quoting reference DE/9564.
 from __future__ import print_function
 import sys
-import os
 import glob
-
-setAvailable = True
-if sys.version_info < (2, 4):
-    import sets
-    from sets import Set
-    setAvailable = False
-
+from builtins import range
 
 def usage():
     print("Usage: $0 [-extension/extensions] <list of names>")
@@ -94,45 +87,57 @@ def isImage(input, allExtensions):
 def removeImageExtension(input, allExtensions):
     return isImage(input, allExtensions)[1]
 
-if len(sys.argv) <= 1:
-    usage()
 
-deleteExtensions = True
-primaryExtensions = ['.nii.gz', '.nii', '.hdr.gz', '.hdr']
-secondaryExtensions = ['.img.gz', '.img']
-allExtensions = primaryExtensions+secondaryExtensions
-validExtensions = primaryExtensions
-startingArg = 1
+def main():
+    if len(sys.argv) <= 1:
+        usage()
+
+    if sys.version_info < (2, 4):
+        import sets
+        from sets import Set
+        setAvailable = False
+    else:
+        setAvailable = True
+
+    deleteExtensions = True
+    primaryExtensions = ['.nii.gz', '.nii', '.hdr.gz', '.hdr']
+    secondaryExtensions = ['.img.gz', '.img']
+    allExtensions = primaryExtensions+secondaryExtensions
+    validExtensions = primaryExtensions
+    startingArg = 1
+
+    if sys.argv[1] == "-extensions":
+        validExtensions = allExtensions
+        deleteExtensions = False
+        startingArg = 2
+    if sys.argv[1] == "-extension":
+        deleteExtensions = False
+        startingArg = 2
 
-if sys.argv[1] == "-extensions":
-    validExtensions = allExtensions
-    deleteExtensions = False
-    startingArg = 2
-if sys.argv[1] == "-extension":
-    deleteExtensions = False
-    startingArg = 2
+    filelist = []
+    for arg in range(startingArg, len(sys.argv)):
+        #      if isImage(sys.argv[arg],allExtensions)[0]:          #These enable a "pedantic" style mode currently not used
+        #         filelist.extend(glob.glob(sys.argv[arg]))
+        #      else:
+        #         for currentExtension in validExtensions:
+        #            filelist.extend(glob.glob(sys.argv[arg]+currentExtension))
+        for currentExtension in validExtensions:
+            filelist.extend(
+                glob.glob(removeImageExtension(sys.argv[arg], allExtensions)+currentExtension))
 
-filelist = []
-for arg in range(startingArg, len(sys.argv)):
-    #      if isImage(sys.argv[arg],allExtensions)[0]:          #These enable a "pedantic" style mode currently not used
-    #         filelist.extend(glob.glob(sys.argv[arg]))
-    #      else:
-    #         for currentExtension in validExtensions:
-    #            filelist.extend(glob.glob(sys.argv[arg]+currentExtension))
-    for currentExtension in validExtensions:
-        filelist.extend(
-            glob.glob(removeImageExtension(sys.argv[arg], allExtensions)+currentExtension))
+    if deleteExtensions:
+        for file in range(0, len(filelist)):
+            filelist[file] = removeImageExtension(filelist[file], allExtensions)
+    if setAvailable:
+        filelist = list(set(filelist))
+    else:
+        filelist = list(Set(filelist))
+    filelist.sort()
 
-if deleteExtensions:
     for file in range(0, len(filelist)):
-        filelist[file] = removeImageExtension(filelist[file], allExtensions)
-if setAvailable:
-    filelist = list(set(filelist))
-else:
-    filelist = list(Set(filelist))
-filelist.sort()
+        print(filelist[file], end=' ')
+        if file < len(filelist)-1:
+            print(" ", end=' ')
 
-for file in range(0, len(filelist)):
-    print(filelist[file], end=' ')
-    if file < len(filelist)-1:
-        print(" ", end=' ')
+if __name__ == "__main__":
+    main()

From 4b67fe03c3eef825215540f6e16660e6948ea464 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Mar 2017 10:06:24 -0700
Subject: [PATCH 02/11] deep revision of old failures

---
 .circle/tests.sh             |  4 ++--
 .coveragerc                  | 25 +++++++++++++++++++++----
 .dockerignore                | 10 +++++-----
 codecov.yml                  |  4 ++++
 docker/files/run_examples.sh | 22 +++++++---------------
 docker/files/run_pytests.sh  | 18 ++++++++++--------
 pytest.ini                   |  3 +++
 7 files changed, 52 insertions(+), 34 deletions(-)
 create mode 100644 pytest.ini

diff --git a/.circle/tests.sh b/.circle/tests.sh
index 51a7957259..bcdbd5eadb 100644
--- a/.circle/tests.sh
+++ b/.circle/tests.sh
@@ -17,8 +17,8 @@ fi
 # They may need to be rebalanced in the future.
 case ${CIRCLE_NODE_INDEX} in
   0)
-    docker run --rm -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /src/nipype nipype/nipype:py27 /usr/bin/run_pytests.sh py27 && \
-    docker run --rm -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /src/nipype nipype/nipype:py35 /usr/bin/run_pytests.sh py35 && \
+    docker run --rm -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_pytests.sh && \
+    docker run --rm -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_pytests.sh && \
     docker run --rm -it -v $WORKDIR:/work -w /src/nipype/doc nipype/nipype:py35 /usr/bin/run_builddocs.sh && \
     docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d && \
     docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
diff --git a/.coveragerc b/.coveragerc
index 80af6f0119..87c2c53b02 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,7 +1,24 @@
 [run]
 branch = True
-include = */nipype/*
+source = nipype/
 omit =
-    */nipype/external/*
-    */nipype/fixes/*
-    */setup.py
+    external/*
+    fixes/*
+    */tests/*
+
+[report]
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
\ No newline at end of file
diff --git a/.dockerignore b/.dockerignore
index 2140bfcb66..35daadb7e1 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -1,6 +1,7 @@
 # python cache
-__pycache__/**/*
 __pycache__
+**/__pycache__
+**/*.pyc
 *.pyc
 
 # python distribution
@@ -26,11 +27,10 @@ docs/
 .circle/**/*
 .circle/
 circle.yml
-.coverage
-.coveragerc
-codecov.yml
 rtd_requirements.txt
 Vagrantfile
 .travis.yml
-.noserc
+.mailmap
 
+# Previous coverage results
+.coverage
\ No newline at end of file
diff --git a/codecov.yml b/codecov.yml
index e2fbd5b0b0..2724855129 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -22,3 +22,7 @@ coverage:
         threshold: 100
         flags:
           - "smoketests"
+  ignore:          # files and folders that will be removed during processing
+    - "nipype/external/*"
+    - "tools/*"
+    - "doc/*"
\ No newline at end of file
diff --git a/docker/files/run_examples.sh b/docker/files/run_examples.sh
index e30ca221c6..bc2c4583c3 100644
--- a/docker/files/run_examples.sh
+++ b/docker/files/run_examples.sh
@@ -17,23 +17,15 @@ echo "log_to_file = true" >> ${HOME}/.nipype/nipype.cfg
 echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/nipype.cfg
 
 # Set up coverage
-echo "[run]" >> .coveragerc
-echo "branch = True" >> .coveragerc
-echo "source = /src/nipype" >> .coveragerc
-echo "include = */nipype/*" >> .coveragerc
-echo "omit =" >> .coveragerc
-echo "    */nipype/external/*" >> .coveragerc
-echo "    */nipype/fixes/*" >> .coveragerc
-echo "    */setup.py" >> .coveragerc
+sed -i -E "s/(source = ).*'/\1\/src\/nipype\/nipype/" /src/nipype/.coveragerc
 
-
-parallel=""
 if [ "$2" == "MultiProc" ]; then
-	parallel="--concurrency=multiprocessing"
+	echo "concurrency = multiprocessing" >> /src/nipype/.coveragerc
 fi
 
-coverage run ${parallel} /src/nipype/tools/run_examples.py $@
-test_exit=$?
-coverage xml -o "${WORKDIR}/smoketest_${example_id}.xml"
+coverage run --rcfile=/src/nipype/.coveragerc /src/nipype/tools/run_examples.py $@
+exit_code=$?
+
+coverage xml -o ${WORKDIR}/smoketest_${example_id}.xml || true
 
-exit $test_exit
\ No newline at end of file
+exit $exit_code
diff --git a/docker/files/run_pytests.sh b/docker/files/run_pytests.sh
index 3b4b99786f..d3640a5898 100644
--- a/docker/files/run_pytests.sh
+++ b/docker/files/run_pytests.sh
@@ -21,19 +21,21 @@ if [[ "${PYTHON_VERSION}" -lt "30" ]]; then
     echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg
 fi
 
-cd /src/nipype/
-make clean
 # Run tests using pytest
-py.test -n ${CIRCLE_NCPUS:-4} --doctest-modules --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}.xml --cov=nipype nipype
-
+py.test -n ${CIRCLE_NCPUS:-1} -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}.xml --cov-config /src/nipype/.coveragerc --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}.xml /src/nipype/
+exit_code=$?
 
 # Workaround: run here the profiler tests in python 3
 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
     echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
     echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg
-    py.test -n ${CIRCLE_NCPUS:-4} --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_profiler.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_profiler.xml --cov=nipype nipype/interfaces/tests/test_runtime_profiler.py
-    py.test -n ${CIRCLE_NCPUS:-4} --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_multiproc.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_multiproc.xml --cov=nipype nipype/pipeline/plugins/tests/test_multiproc*.py
+    py.test -n ${CIRCLE_NCPUS:-1} -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_profiler.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_profiler.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py && \
+    py.test -n ${CIRCLE_NCPUS:-1} -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_multiproc.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_multiproc.xml /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py
+    exit_code = $(( $exit_code + $?))
 fi
 
-# Copy crashfiles to scratch
-find /src/nipype/ -name "crash-*" -exec cp {} ${WORKDIR}/crashfiles/ \;
+find /src/nipype/ -name "crash-*" -exec mv {} ${WORKDIR}/crashfiles/ \;
+
+# Just in case output xml files are misplaced,
+# then circle would not tell the tests failed otherwise
+exit $exit_code
diff --git a/pytest.ini b/pytest.ini
new file mode 100644
index 0000000000..0f91b25324
--- /dev/null
+++ b/pytest.ini
@@ -0,0 +1,3 @@
+[pytest]
+norecursedirs = .git build dist doc nipype/external tools examples tools
+addopts = --doctest-modules
\ No newline at end of file

From 1357579cf514b841a98c37372e1d88515519a8b3 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Mar 2017 11:27:48 -0700
Subject: [PATCH 03/11] fix failing tests

---
 .coveragerc                    |  1 +
 docker/files/run_examples.sh   |  4 +++-
 nipype/utils/tests/test_cmd.py | 21 +++------------------
 3 files changed, 7 insertions(+), 19 deletions(-)

diff --git a/.coveragerc b/.coveragerc
index 87c2c53b02..35c3eccee6 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,5 +1,6 @@
 [run]
 branch = True
+data_file = .coverage
 source = nipype/
 omit =
     external/*
diff --git a/docker/files/run_examples.sh b/docker/files/run_examples.sh
index bc2c4583c3..063b35e7d2 100644
--- a/docker/files/run_examples.sh
+++ b/docker/files/run_examples.sh
@@ -17,7 +17,9 @@ echo "log_to_file = true" >> ${HOME}/.nipype/nipype.cfg
 echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/nipype.cfg
 
 # Set up coverage
+export COVERAGE_PROCESS_START=/src/nipype/.coveragerc
 sed -i -E "s/(source = ).*'/\1\/src\/nipype\/nipype/" /src/nipype/.coveragerc
+sed -i -E "s/(data_file = ).*'/\1\/\/work\/.coverage/" /src/nipype/.coveragerc
 
 if [ "$2" == "MultiProc" ]; then
 	echo "concurrency = multiprocessing" >> /src/nipype/.coveragerc
@@ -26,6 +28,6 @@ fi
 coverage run --rcfile=/src/nipype/.coveragerc /src/nipype/tools/run_examples.py $@
 exit_code=$?
 
-coverage xml -o ${WORKDIR}/smoketest_${example_id}.xml || true
+coverage xml --rcfile=/src/nipype/.coveragerc -o ${WORKDIR}/smoketest_${example_id}.xml || true
 
 exit $exit_code
diff --git a/nipype/utils/tests/test_cmd.py b/nipype/utils/tests/test_cmd.py
index e6aad61b28..fc182f1f9f 100644
--- a/nipype/utils/tests/test_cmd.py
+++ b/nipype/utils/tests/test_cmd.py
@@ -12,7 +12,6 @@
 from ...utils import nipype_cmd
 
 PY3 = sys.version_info[0] >= 3
-PY2 = sys.version_info[0] < 2
 
 @contextmanager
 def capture_sys_output():
@@ -35,20 +34,11 @@ def test_main_returns_2_on_empty(self):
 
         exit_exception = cm.value
         assert exit_exception.code == 2
-
-        if PY2:
-            assert stderr.getvalue() == \
-                """usage: nipype_cmd [-h] module interface
+        assert stderr.getvalue() == \
+            """usage: nipype_cmd [-h] module interface
 nipype_cmd: error: too few arguments
-"""
-        elif PY3:
-            assert stderr.getvalue() == \
-                """usage: nipype_cmd [-h] module interface
-nipype_cmd: error: the following arguments are required: module, interface
 """
 
-        assert stdout.getvalue() == ''
-
     def test_main_returns_0_on_help(self):
         with pytest.raises(SystemExit) as cm:
             with capture_sys_output() as (stdout, stderr):
@@ -115,12 +105,7 @@ def test_run_4d_realign_without_arguments(self):
                                                        in_file [in_file ...]
                                                        tr"""
 
-        if PY3:
-            error_message += """
-nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: the following arguments are required: in_file, tr
-"""
-        else:
-            error_message += """
+        error_message += """
 nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: too few arguments
 """
 

From 7b6791141f61d80af6b0811eba6e3dca3e4ad794 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Mar 2017 12:06:42 -0700
Subject: [PATCH 04/11] fix error in run_pytests, trying to get coverage to
 track examples

---
 .coveragerc                 | 9 ++++++---
 docker/files/run_pytests.sh | 4 ++--
 pytest.ini                  | 2 +-
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/.coveragerc b/.coveragerc
index 35c3eccee6..90a812a425 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,11 +1,14 @@
 [run]
 branch = True
 data_file = .coverage
-source = nipype/
+source = .
 omit =
-    external/*
-    fixes/*
+    nipype/external/*
+    nipype/fixes/*
+    tools/*
     */tests/*
+include =
+    tools/run_exaples.py
 
 [report]
 exclude_lines =
diff --git a/docker/files/run_pytests.sh b/docker/files/run_pytests.sh
index d3640a5898..5ff6f910f4 100644
--- a/docker/files/run_pytests.sh
+++ b/docker/files/run_pytests.sh
@@ -31,11 +31,11 @@ if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
     echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg
     py.test -n ${CIRCLE_NCPUS:-1} -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_profiler.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_profiler.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py && \
     py.test -n ${CIRCLE_NCPUS:-1} -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_multiproc.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_multiproc.xml /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py
-    exit_code = $(( $exit_code + $?))
+    exit_code=$(( $exit_code + $?))
 fi
 
 find /src/nipype/ -name "crash-*" -exec mv {} ${WORKDIR}/crashfiles/ \;
 
 # Just in case output xml files are misplaced,
 # then circle would not tell the tests failed otherwise
-exit $exit_code
+exit ${exit_code}
diff --git a/pytest.ini b/pytest.ini
index 0f91b25324..46148ace22 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,3 +1,3 @@
 [pytest]
-norecursedirs = .git build dist doc nipype/external tools examples tools
+norecursedirs = .git build dist doc nipype/external tools examples tools src
 addopts = --doctest-modules
\ No newline at end of file

From 00095c4cc9ab2cce33c59784c7b97ac3f2768b1c Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Mar 2017 15:37:47 -0700
Subject: [PATCH 05/11] fix typo in .coveragerc

---
 .coveragerc                 | 3 ++-
 docker/files/run_pytests.sh | 2 +-
 pytest.ini                  | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.coveragerc b/.coveragerc
index 90a812a425..86848c0d61 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -6,9 +6,10 @@ omit =
     nipype/external/*
     nipype/fixes/*
     tools/*
+    doc/*
     */tests/*
 include =
-    tools/run_exaples.py
+    tools/run_examples.py
 
 [report]
 exclude_lines =
diff --git a/docker/files/run_pytests.sh b/docker/files/run_pytests.sh
index 5ff6f910f4..bbcf2734db 100644
--- a/docker/files/run_pytests.sh
+++ b/docker/files/run_pytests.sh
@@ -31,7 +31,7 @@ if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
     echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg
     py.test -n ${CIRCLE_NCPUS:-1} -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_profiler.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_profiler.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py && \
     py.test -n ${CIRCLE_NCPUS:-1} -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_multiproc.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_multiproc.xml /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py
-    exit_code=$(( $exit_code + $?))
+    exit_code=$(( $exit_code + $? ))
 fi
 
 find /src/nipype/ -name "crash-*" -exec mv {} ${WORKDIR}/crashfiles/ \;
diff --git a/pytest.ini b/pytest.ini
index 46148ace22..6247b04cca 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,3 +1,3 @@
 [pytest]
-norecursedirs = .git build dist doc nipype/external tools examples tools src
+norecursedirs = .git build dist doc nipype/external tools examples src
 addopts = --doctest-modules
\ No newline at end of file

From ea6bdc312c68fc680fb805b66100dab18e7e63ad Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Mar 2017 17:46:35 -0700
Subject: [PATCH 06/11] hopefully, final fix to the circle deployment

* fixed nipypecmd tests
* removed -n from py.test, which was making py.test think all tests passed (when some were failing)
* fixed the coverage collection when running the examples
---
 .coveragerc                    | 27 ---------------------------
 docker/files/run_examples.sh   |  9 ++++-----
 docker/files/run_pytests.sh    |  9 ++++++---
 nipype/info.py                 |  1 -
 nipype/utils/tests/test_cmd.py | 20 ++++++++++++++++----
 5 files changed, 26 insertions(+), 40 deletions(-)

diff --git a/.coveragerc b/.coveragerc
index 86848c0d61..398ff08afa 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,29 +1,2 @@
 [run]
 branch = True
-data_file = .coverage
-source = .
-omit =
-    nipype/external/*
-    nipype/fixes/*
-    tools/*
-    doc/*
-    */tests/*
-include =
-    tools/run_examples.py
-
-[report]
-exclude_lines =
-    # Have to re-enable the standard pragma
-    pragma: no cover
-
-    # Don't complain about missing debug-only code:
-    def __repr__
-    if self\.debug
-
-    # Don't complain if tests don't hit defensive assertion code:
-    raise AssertionError
-    raise NotImplementedError
-
-    # Don't complain if non-runnable code isn't run:
-    if 0:
-    if __name__ == .__main__.:
\ No newline at end of file
diff --git a/docker/files/run_examples.sh b/docker/files/run_examples.sh
index 063b35e7d2..0018c2b5b0 100644
--- a/docker/files/run_examples.sh
+++ b/docker/files/run_examples.sh
@@ -17,17 +17,16 @@ echo "log_to_file = true" >> ${HOME}/.nipype/nipype.cfg
 echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/nipype.cfg
 
 # Set up coverage
-export COVERAGE_PROCESS_START=/src/nipype/.coveragerc
-sed -i -E "s/(source = ).*'/\1\/src\/nipype\/nipype/" /src/nipype/.coveragerc
-sed -i -E "s/(data_file = ).*'/\1\/\/work\/.coverage/" /src/nipype/.coveragerc
+export COVERAGE_FILE=${WORKDIR}/.coverage_${example_id}
+#sed -i -E "s/(source = ).*'/\1\/src\/nipype\/nipype/" /src/nipype/.coveragerc
 
 if [ "$2" == "MultiProc" ]; then
 	echo "concurrency = multiprocessing" >> /src/nipype/.coveragerc
 fi
 
-coverage run --rcfile=/src/nipype/.coveragerc /src/nipype/tools/run_examples.py $@
+coverage run /src/nipype/tools/run_examples.py $@
 exit_code=$?
 
-coverage xml --rcfile=/src/nipype/.coveragerc -o ${WORKDIR}/smoketest_${example_id}.xml || true
+coverage xml -o ${WORKDIR}/smoketest_${example_id}.xml || true
 
 exit $exit_code
diff --git a/docker/files/run_pytests.sh b/docker/files/run_pytests.sh
index bbcf2734db..1c88a6594a 100644
--- a/docker/files/run_pytests.sh
+++ b/docker/files/run_pytests.sh
@@ -3,6 +3,8 @@ set -e
 set -x
 set -u
 
+
+TESTPATH=${1:-/src/nipype/}
 WORKDIR=${WORK:-/work}
 PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" )
 
@@ -22,15 +24,16 @@ if [[ "${PYTHON_VERSION}" -lt "30" ]]; then
 fi
 
 # Run tests using pytest
-py.test -n ${CIRCLE_NCPUS:-1} -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}.xml --cov-config /src/nipype/.coveragerc --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}.xml /src/nipype/
+export COVERAGE_FILE=${WORKDIR}/.coverage_py${PYTHON_VERSION}
+py.test -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}.xml --cov nipype --cov-config /src/nipype/.coveragerc --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}.xml ${TESTPATH}
 exit_code=$?
 
 # Workaround: run here the profiler tests in python 3
 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
     echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
     echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg
-    py.test -n ${CIRCLE_NCPUS:-1} -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_profiler.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_profiler.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py && \
-    py.test -n ${CIRCLE_NCPUS:-1} -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_multiproc.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_multiproc.xml /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py
+    export COVERAGE_FILE=${WORKDIR}/.coverage_py${PYTHON_VERSION}_extra
+    py.test -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py
     exit_code=$(( $exit_code + $? ))
 fi
 
diff --git a/nipype/info.py b/nipype/info.py
index c170d3800c..81a8adce0a 100644
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -144,7 +144,6 @@ def get_nipype_gitversion():
 TESTS_REQUIRES = [
     'pytest>=%s' % PYTEST_MIN_VERSION,
     'pytest-cov',
-    'pytest-xdist',
     'mock',
     'codecov',
     'dipy',
diff --git a/nipype/utils/tests/test_cmd.py b/nipype/utils/tests/test_cmd.py
index fc182f1f9f..315d55441f 100644
--- a/nipype/utils/tests/test_cmd.py
+++ b/nipype/utils/tests/test_cmd.py
@@ -11,7 +11,7 @@
 from io import StringIO
 from ...utils import nipype_cmd
 
-PY3 = sys.version_info[0] >= 3
+PY2 = sys.version_info[0] < 3
 
 @contextmanager
 def capture_sys_output():
@@ -34,10 +34,17 @@ def test_main_returns_2_on_empty(self):
 
         exit_exception = cm.value
         assert exit_exception.code == 2
-        assert stderr.getvalue() == \
-            """usage: nipype_cmd [-h] module interface
+
+        msg = """usage: nipype_cmd [-h] module interface
+nipype_cmd: error: the following arguments are required: module, interface
+"""
+
+        if PY2:
+            msg = """usage: nipype_cmd [-h] module interface
 nipype_cmd: error: too few arguments
 """
+        assert stderr.getvalue() == msg
+        assert stdout.getvalue() == ''
 
     def test_main_returns_0_on_help(self):
         with pytest.raises(SystemExit) as cm:
@@ -105,7 +112,12 @@ def test_run_4d_realign_without_arguments(self):
                                                        in_file [in_file ...]
                                                        tr"""
 
-        error_message += """
+        if not PY2:
+            error_message += """
+nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: the following arguments are required: in_file, tr
+"""
+        else:
+            error_message += """
 nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: too few arguments
 """
 

From 0041e6bea6d34903a49b2bb41ae999c6bb007d90 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Mar 2017 18:35:24 -0700
Subject: [PATCH 07/11] add -v flag in travis (after the segfault)

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

diff --git a/.travis.yml b/.travis.yml
index 64b7fea960..84973174db 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -42,7 +42,7 @@ before_install:
 install:
 - travis_retry pip install -e .[$NIPYPE_EXTRAS]
 script:
-- py.test --doctest-modules nipype
+- py.test -v --doctest-modules .
 deploy:
   provider: pypi
   user: satra

From e70181176bf8564380d7867de20551e9ad499c83 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Mar 2017 18:35:44 -0700
Subject: [PATCH 08/11] add .cache to dockerignore

---
 .dockerignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.dockerignore b/.dockerignore
index 35daadb7e1..c44710d14e 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -24,6 +24,7 @@ src/
 # other
 docs/**/*
 docs/
+.cache/
 .circle/**/*
 .circle/
 circle.yml

From bca19820518e13d23f17023a24924839ea4e85f1 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Mar 2017 18:56:34 -0700
Subject: [PATCH 09/11] add --rm=false in docker run commands

---
 .circle/tests.sh | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/.circle/tests.sh b/.circle/tests.sh
index bcdbd5eadb..ad7aed6d9f 100644
--- a/.circle/tests.sh
+++ b/.circle/tests.sh
@@ -17,23 +17,23 @@ fi
 # They may need to be rebalanced in the future.
 case ${CIRCLE_NODE_INDEX} in
   0)
-    docker run --rm -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_pytests.sh && \
-    docker run --rm -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_pytests.sh && \
-    docker run --rm -it -v $WORKDIR:/work -w /src/nipype/doc nipype/nipype:py35 /usr/bin/run_builddocs.sh && \
-    docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d && \
-    docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
+    docker run --rm=false -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_pytests.sh && \
+    docker run --rm=false -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_pytests.sh && \
+    docker run --rm=false -it -v $WORKDIR:/work -w /src/nipype/doc nipype/nipype:py35 /usr/bin/run_builddocs.sh && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
     ;;
   1)
-    docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ level1 && \
-    docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ l2pipeline
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ level1 && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ l2pipeline
     ;;
   2)
-    docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
-    docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
+    docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
+    docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
     ;;
   3)
-    docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
-    docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline && \
-    docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow
+    docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline && \
+    docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow
     ;;
 esac

From e903dfe1c27609aad600d6a024902b34d0cb8e3e Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Mar 2017 20:56:42 -0700
Subject: [PATCH 10/11] fix travis, keep coverage reports in artifacts

---
 .circle/codecov.sh           |  9 ++++-----
 .travis.yml                  |  2 +-
 circle.yml                   |  1 +
 docker/files/run_examples.sh |  8 ++++----
 docker/files/run_pytests.sh  | 10 +++++-----
 5 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/.circle/codecov.sh b/.circle/codecov.sh
index 84df39c1c2..d7c0156372 100644
--- a/.circle/codecov.sh
+++ b/.circle/codecov.sh
@@ -13,13 +13,12 @@ set -x         # Print command traces before executing command.
 curl -so codecov.io https://codecov.io/bash
 chmod 755 codecov.io
 
-find "${WORKDIR}/" -name 'coverage*.xml' -maxdepth 1 -print0 | \
+find "${WORKDIR}/tests/" -name 'coverage*.xml' -maxdepth 1 -print0 | \
   xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F unittests
-find "${WORKDIR}/" -name 'smoketest*.xml' -maxdepth 1 -print0 | \
+find "${WORKDIR}/tests/" -name 'smoketest*.xml' -maxdepth 1 -print0 | \
   xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F smoketests
 
 # Place test and coverage in the tests folder
 mkdir -p ${CIRCLE_TEST_REPORTS}/tests/
-cp ${WORKDIR}/pytest*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
-cp ${WORKDIR}/coverage*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
-cp ${WORKDIR}/smoketest*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
+cp ${WORKDIR}/tests/*.xml ${CIRCLE_TEST_REPORTS}/tests/
+
diff --git a/.travis.yml b/.travis.yml
index 84973174db..bef97b9b59 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -42,7 +42,7 @@ before_install:
 install:
 - travis_retry pip install -e .[$NIPYPE_EXTRAS]
 script:
-- py.test -v --doctest-modules .
+- py.test -v --doctest-modules nipype
 deploy:
   provider: pypi
   user: satra
diff --git a/circle.yml b/circle.yml
index 24eaed8e2d..a8b9baf7d6 100644
--- a/circle.yml
+++ b/circle.yml
@@ -56,6 +56,7 @@ general:
   artifacts:
     - "~/work/docs"
     - "~/work/logs"
+    - "~/work/tests"
 
 deployment:
   production:
diff --git a/docker/files/run_examples.sh b/docker/files/run_examples.sh
index 0018c2b5b0..a384eb60bf 100644
--- a/docker/files/run_examples.sh
+++ b/docker/files/run_examples.sh
@@ -8,7 +8,7 @@ arr=$@
 tmp_var=$( IFS=$' '; echo "${arr[*]}" )
 example_id=${tmp_var//[^A-Za-z0-9_-]/_}
 
-mkdir -p ${HOME}/.nipype ${WORKDIR}/logs/example_${example_id}
+mkdir -p ${HOME}/.nipype ${WORKDIR}/logs/example_${example_id} ${WORKDIR}/tests
 echo "[logging]" > ${HOME}/.nipype/nipype.cfg
 echo "workflow_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
 echo "interface_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
@@ -17,7 +17,7 @@ echo "log_to_file = true" >> ${HOME}/.nipype/nipype.cfg
 echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/nipype.cfg
 
 # Set up coverage
-export COVERAGE_FILE=${WORKDIR}/.coverage_${example_id}
+export COVERAGE_FILE=${WORKDIR}/tests/.coverage_${example_id}
 #sed -i -E "s/(source = ).*'/\1\/src\/nipype\/nipype/" /src/nipype/.coveragerc
 
 if [ "$2" == "MultiProc" ]; then
@@ -27,6 +27,6 @@ fi
 coverage run /src/nipype/tools/run_examples.py $@
 exit_code=$?
 
-coverage xml -o ${WORKDIR}/smoketest_${example_id}.xml || true
-
+coverage xml -o ${WORKDIR}/tests/smoketest_${example_id}.xml
 exit $exit_code
+
diff --git a/docker/files/run_pytests.sh b/docker/files/run_pytests.sh
index 1c88a6594a..b6d7f49383 100644
--- a/docker/files/run_pytests.sh
+++ b/docker/files/run_pytests.sh
@@ -9,7 +9,7 @@ WORKDIR=${WORK:-/work}
 PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" )
 
 # Create necessary directories
-mkdir -p ${WORKDIR}/crashfiles ${WORKDIR}/logs/py${PYTHON_VERSION}
+mkdir -p ${WORKDIR}/tests ${WORKDIR}/crashfiles ${WORKDIR}/logs/py${PYTHON_VERSION}
 
 # Create a nipype config file
 mkdir -p ${HOME}/.nipype
@@ -24,16 +24,16 @@ if [[ "${PYTHON_VERSION}" -lt "30" ]]; then
 fi
 
 # Run tests using pytest
-export COVERAGE_FILE=${WORKDIR}/.coverage_py${PYTHON_VERSION}
-py.test -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}.xml --cov nipype --cov-config /src/nipype/.coveragerc --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}.xml ${TESTPATH}
+export COVERAGE_FILE=${WORKDIR}/tests/.coverage_py${PYTHON_VERSION}
+py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}.xml --cov nipype --cov-config /src/nipype/.coveragerc --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}.xml ${TESTPATH}
 exit_code=$?
 
 # Workaround: run here the profiler tests in python 3
 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
     echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
     echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg
-    export COVERAGE_FILE=${WORKDIR}/.coverage_py${PYTHON_VERSION}_extra
-    py.test -v --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py
+    export COVERAGE_FILE=${WORKDIR}/tests/.coverage_py${PYTHON_VERSION}_extra
+    py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py
     exit_code=$(( $exit_code + $? ))
 fi
 

From 2a4f1570d64ae06d662f25179effbcc86809c6e6 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Mar 2017 21:41:03 -0700
Subject: [PATCH 11/11] split codecov and test reports, keep crashfiles as
 artifacts

---
 .circle/codecov.sh           | 4 ----
 circle.yml                   | 3 +++
 docker/files/run_examples.sh | 8 ++++----
 docker/files/run_pytests.sh  | 6 +++---
 4 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/.circle/codecov.sh b/.circle/codecov.sh
index d7c0156372..2e895dfea8 100644
--- a/.circle/codecov.sh
+++ b/.circle/codecov.sh
@@ -18,7 +18,3 @@ find "${WORKDIR}/tests/" -name 'coverage*.xml' -maxdepth 1 -print0 | \
 find "${WORKDIR}/tests/" -name 'smoketest*.xml' -maxdepth 1 -print0 | \
   xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F smoketests
 
-# Place test and coverage in the tests folder
-mkdir -p ${CIRCLE_TEST_REPORTS}/tests/
-cp ${WORKDIR}/tests/*.xml ${CIRCLE_TEST_REPORTS}/tests/
-
diff --git a/circle.yml b/circle.yml
index a8b9baf7d6..6a75f29446 100644
--- a/circle.yml
+++ b/circle.yml
@@ -49,6 +49,8 @@ test:
         timeout: 7200
         parallel: true
   post:
+    # Place reports in the appropriate folder
+    - mkdir -p ${CIRCLE_TEST_REPORTS}/tests/ && cp ${WORKDIR}/tests/*.xml ${CIRCLE_TEST_REPORTS}/tests/
     # Send coverage data to codecov.io
     - bash .circle/codecov.sh
 
@@ -57,6 +59,7 @@ general:
     - "~/work/docs"
     - "~/work/logs"
     - "~/work/tests"
+    - "~/work/crashfiles"
 
 deployment:
   production:
diff --git a/docker/files/run_examples.sh b/docker/files/run_examples.sh
index a384eb60bf..a23c27e76b 100644
--- a/docker/files/run_examples.sh
+++ b/docker/files/run_examples.sh
@@ -8,7 +8,7 @@ arr=$@
 tmp_var=$( IFS=$' '; echo "${arr[*]}" )
 example_id=${tmp_var//[^A-Za-z0-9_-]/_}
 
-mkdir -p ${HOME}/.nipype ${WORKDIR}/logs/example_${example_id} ${WORKDIR}/tests
+mkdir -p ${HOME}/.nipype ${WORKDIR}/logs/example_${example_id} ${WORKDIR}/tests ${WORKDIR}/crashfiles
 echo "[logging]" > ${HOME}/.nipype/nipype.cfg
 echo "workflow_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
 echo "interface_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
@@ -17,9 +17,7 @@ echo "log_to_file = true" >> ${HOME}/.nipype/nipype.cfg
 echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/nipype.cfg
 
 # Set up coverage
-export COVERAGE_FILE=${WORKDIR}/tests/.coverage_${example_id}
-#sed -i -E "s/(source = ).*'/\1\/src\/nipype\/nipype/" /src/nipype/.coveragerc
-
+export COVERAGE_FILE=${WORKDIR}/tests/.coverage.${example_id}
 if [ "$2" == "MultiProc" ]; then
 	echo "concurrency = multiprocessing" >> /src/nipype/.coveragerc
 fi
@@ -27,6 +25,8 @@ fi
 coverage run /src/nipype/tools/run_examples.py $@
 exit_code=$?
 
+# Collect crashfiles and generate xml report
 coverage xml -o ${WORKDIR}/tests/smoketest_${example_id}.xml
+find /work -name "crash-*" -maxdepth 1 -exec mv {} ${WORKDIR}/crashfiles/ \;
 exit $exit_code
 
diff --git a/docker/files/run_pytests.sh b/docker/files/run_pytests.sh
index b6d7f49383..a0e6424950 100644
--- a/docker/files/run_pytests.sh
+++ b/docker/files/run_pytests.sh
@@ -24,7 +24,7 @@ if [[ "${PYTHON_VERSION}" -lt "30" ]]; then
 fi
 
 # Run tests using pytest
-export COVERAGE_FILE=${WORKDIR}/tests/.coverage_py${PYTHON_VERSION}
+export COVERAGE_FILE=${WORKDIR}/tests/.coverage.py${PYTHON_VERSION}
 py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}.xml --cov nipype --cov-config /src/nipype/.coveragerc --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}.xml ${TESTPATH}
 exit_code=$?
 
@@ -32,12 +32,12 @@ exit_code=$?
 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
     echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
     echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg
-    export COVERAGE_FILE=${WORKDIR}/tests/.coverage_py${PYTHON_VERSION}_extra
+    export COVERAGE_FILE=${WORKDIR}/tests/.coverage.py${PYTHON_VERSION}_extra
     py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py
     exit_code=$(( $exit_code + $? ))
 fi
 
-find /src/nipype/ -name "crash-*" -exec mv {} ${WORKDIR}/crashfiles/ \;
+find /work -name "crash-*" -maxdepth 1 -exec mv {} ${WORKDIR}/crashfiles/ \;
 
 # Just in case output xml files are misplaced,
 # then circle would not tell the tests failed otherwise