run_examples.sh

#!/bin/bash
set -e
set -x
set -u

WORKDIR=${WORKDIR:-/work}
arr=$@
tmp_var=$( IFS=$' '; echo "${arr[*]}" )
example_id=${tmp_var//[^A-Za-z0-9_-]/_}

mkdir -p "${HOME}"/.nipype "${WORKDIR}"/logs/example_"${example_id}" "${WORKDIR}"/tests "${WORKDIR}"/crashfiles
echo "[logging]" > "${HOME}"/.nipype/nipype.cfg
echo "workflow_level = DEBUG" >> "${HOME}"/.nipype/nipype.cfg
echo "interface_level = DEBUG" >> "${HOME}"/.nipype/nipype.cfg
echo "utils_level = DEBUG" >> "${HOME}"/.nipype/nipype.cfg
echo "log_to_file = true" >> "${HOME}"/.nipype/nipype.cfg
echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> "${HOME}"/.nipype/nipype.cfg

echo '[execution]' >> "${HOME}"/.nipype/nipype.cfg
echo 'crashfile_format = txt' >> "${HOME}"/.nipype/nipype.cfg

if [[ "${NIPYPE_RESOURCE_MONITOR:-0}" == "1" ]]; then
    echo '[monitoring]' >> "${HOME}"/.nipype/nipype.cfg
    echo 'enabled = true' >> "${HOME}"/.nipype/nipype.cfg
    echo 'sample_frequency = 3' >> "${HOME}"/.nipype/nipype.cfg
fi

# Set up coverage
export COVERAGE_FILE=${WORKDIR}/tests/.coverage.${example_id}
if [ "$2" == "MultiProc" ]; then
	echo "concurrency = multiprocessing" >> /src/nipype/.coveragerc
fi

coverage run /src/nipype/tools/run_examples.py $@
exit_code=$?

if [[ "${NIPYPE_RESOURCE_MONITOR:-0}" == "1" ]]; then
	cp resource_monitor.json 2>/dev/null "${WORKDIR}"/logs/example_"${example_id}"/ || :
fi
# Collect crashfiles and generate xml report
coverage xml -o "${WORKDIR}"/tests/smoketest_"${example_id}".xml
find /work -maxdepth 1 -name "crash-*" -exec mv {} "${WORKDIR}"/crashfiles/ \;
exit $exit_code