[FIX] CircleCI tests

.circle/codecov.sh

@@ -13,13 +13,8 @@ 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

.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 /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 -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

.coveragerc

@@ -1,7 +1,2 @@
 [run]
 branch = True
-include = */nipype/*
-omit =
-    */nipype/external/*
-    */nipype/fixes/*
-    */setup.py

.dockerignore

@@ -1,6 +1,7 @@
 # python cache
-__pycache__/**/*
 __pycache__
+**/__pycache__
+**/*.pyc
 *.pyc
 
 # python distribution
@@ -23,14 +24,14 @@ src/
 # other
 docs/**/*
 docs/
+.cache/
 .circle/**/*
 .circle/
 circle.yml
-.coverage
-.coveragerc
-codecov.yml
 rtd_requirements.txt
 Vagrantfile
 .travis.yml
-.noserc
+.mailmap
 
+# Previous coverage results
+.coverage

.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 nipype
 deploy:
   provider: pypi
   user: satra

circle.yml

@@ -49,13 +49,17 @@ 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
 
 general:
   artifacts:
     - "~/work/docs"
     - "~/work/logs"
+    - "~/work/tests"
+    - "~/work/crashfiles"
 
 deployment:
   production:

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/*"

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 ${WORKDIR}/crashfiles
 echo "[logging]" > ${HOME}/.nipype/nipype.cfg
 echo "workflow_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
 echo "interface_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
@@ -17,23 +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
-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
-
-
-parallel=""
+export COVERAGE_FILE=${WORKDIR}/tests/.coverage.${example_id}
 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 /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
 
-exit $test_exit

docker/files/run_pytests.sh

@@ -3,11 +3,13 @@ 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]))" )
 
 # 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 ${HOME}/.nipype
@@ -21,19 +23,22 @@ if [[ "${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${PYTHON_VERSION}.xml --cov=nipype nipype
-
+export COVERAGE_FILE=${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
-    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${PYTHON_VERSION}_multiproc.xml --cov=nipype nipype/pipeline/plugins/tests/test_multiproc*.py
+    export COVERAGE_FILE=${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
 
-# Copy crashfiles to scratch
-find /src/nipype/ -name "crash-*" -exec cp {} ${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
+exit ${exit_code}

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()

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',

nipype/utils/tests/test_cmd.py

@@ -11,8 +11,7 @@
 from io import StringIO
 from ...utils import nipype_cmd
 
-PY3 = sys.version_info[0] >= 3
-PY2 = sys.version_info[0] < 2
+PY2 = sys.version_info[0] < 3
 
 @contextmanager
 def capture_sys_output():
@@ -36,17 +35,15 @@ 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
-nipype_cmd: error: too few arguments
-"""
-        elif PY3:
-            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):
@@ -115,7 +112,7 @@ def test_run_4d_realign_without_arguments(self):
                                                        in_file [in_file ...]
                                                        tr"""
 
-        if PY3:
+        if not PY2:
             error_message += """
 nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: the following arguments are required: in_file, tr
 """

pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+norecursedirs = .git build dist doc nipype/external tools examples src
+addopts = --doctest-modules