run_pytests.sh

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


TESTPATH=${1:-/src/nipype/nipype}
WORKDIR=${WORK:-/work}
PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" )

# Create necessary directories
mkdir -p "${WORKDIR}"/tests "${WORKDIR}"/crashfiles "${WORKDIR}"/logs/py"${PYTHON_VERSION}"

# Create a nipype config file
mkdir -p "${HOME}"/.nipype
echo '[logging]' > "${HOME}"/.nipype/nipype.cfg
echo 'log_to_file = true' >> "${HOME}"/.nipype/nipype.cfg
echo "log_directory = ${WORKDIR}/logs/py${PYTHON_VERSION}" >> "${HOME}"/.nipype/nipype.cfg

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

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

# Run tests using pytest
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 \
    -n auto \
    -c "${TESTPATH}"/pytest.ini "${TESTPATH}"
exit_code=$?

# Collect crashfiles
find "${WORKDIR}" -maxdepth 1 -name "crash-*" -exec mv {} "${WORKDIR}"/crashfiles/ \;

echo "Unit tests finished with exit code ${exit_code}"
exit ${exit_code}