deep revision of old failures

Author: oesteban

.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

.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__.:

.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

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

@@ -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
+exit $exit_code

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

pytest.ini

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