jenkins.bash

#!/bin/bash
if [[ -z "${JENKINS_URL}" ]]
then
	echo "Looks like we're not being run by Jenkins, this is dangerous"
	echo "due to use of git clean -fdx command."
	exit 1
fi
venv() {
        if ! test -d "$1" ; then
                virtualenv -p python"${PYTHON_VERSION}" "$1"
        fi
	# shellcheck source=/dev/null
        source "$1"/bin/activate
}

# clean both the repos before the loop
git clean --force -d -x || /bin/true
wget https://github.com/common-workflow-language/common-workflow-language/archive/master.tar.gz
tar xzf master.tar.gz
docker pull node:slim


# Test for Python 2.7 and Python 3
for PYTHON_VERSION in 2 3
do
for CONTAINER in docker
# for CONTAINER in docker singularity
# singularity having issues on ci.commonwl.org; tests pass with https://gist.github.com/mr-c/0ec90d717617d074017c0cb38b72d1a4
do
	venv cwltool-venv${PYTHON_VERSION}
	export PIP_DOWNLOAD_CACHE=/var/lib/jenkins/pypi-cache/
	# use pip2.7 and pip3 in separate loop runs
	pip${PYTHON_VERSION} install -U setuptools wheel pip
	pip${PYTHON_VERSION} uninstall -y cwltool
	pip${PYTHON_VERSION} install -e .
	pip${PYTHON_VERSION} install "cwltest>=1.0.20180518074130" codecov
	pushd common-workflow-language-master
	rm -f .coverage* coverage.xml
	source=$(realpath ../cwltool)
	COVERAGE_RC=${PWD}/.coveragerc
	cat > ${COVERAGE_RC} <<EOF
[run]
branch = True
source = ${source}

[report]
exclude_lines =
    if self.debug:
    pragma: no cover
    raise NotImplementedError
    if __name__ == .__main__.:
ignore_errors = True
omit =
    tests/*
EOF
	CWLTOOL_WITH_COV=${PWD}/cwltool_with_cov${PYTHON_VERSION}
	cat > ${CWLTOOL_WITH_COV} <<EOF
#!/bin/bash
coverage run --parallel-mode --rcfile=${COVERAGE_RC} \
	"$(which cwltool)" "\$@"
EOF
	chmod a+x ${CWLTOOL_WITH_COV}
	EXTRA="--parallel"
	# shellcheck disable=SC2154
	if [[ "$version" = *dev* ]]
	then
		EXTRA+=" --enable-dev"
	fi
	if [[ "$CONTAINER" = "singularity" ]]
	then
		EXTRA+=" --singularity"
	fi
	if [ -n "$EXTRA" ]
	then
		EXTRA="EXTRA=${EXTRA}"
	fi
	# shellcheck disable=SC2086
	LC_ALL=C.UTF-8 ./run_test.sh --junit-xml=result${PYTHON_VERSION}.xml \
		RUNNER=${CWLTOOL_WITH_COV} "-j$(($(nproc) / 2))"\
		DRAFT="${version}" "${EXTRA}" \
		"--classname=py${PYTHON_VERSION}_${CONTAINER}"
	# LC_ALL=C is to work around junit-xml ASCII only bug
	CODE=$((CODE+$?)) # capture return code of ./run_test.sh
	coverage combine "--rcfile=${COVERAGE_RC}" $(find . -name '.coverage.*')
	coverage xml "--rcfile=${COVERAGE_RC}"
	codecov --file coverage.xml
	deactivate
	popd
done
done
# build new docker container
if [ "$GIT_BRANCH" = "origin/master" ] && [[ "$version" = "v1.0" ]]
then
  ./build-cwl-docker.sh
fi
#docker rm -v $(docker ps -a -f status=exited | sed 's/  */ /g' | cut -d' ' -f1)
exit ${CODE}