jenkins-build.sh

#!/bin/bash

cov_analysis_dir=/usr/local/cov-analysis-linux64-6.6.1/bin
cov_analysis_bin=cov-build

rm -Rf .env build dist khmer/_khmermodule.so cov-int

virtualenv .env

. .env/bin/activate

make clean

unset coverage_pre coverage_post coverity

if [[ "${NODE_LABELS}" == *linux* ]]
then
	if type gcov >/dev/null 2>&1
	then
		export CFLAGS="-pg -fprofile-arcs -ftest-coverage"
		coverage_post='--debug --inplace --libraries gcov'
	else
		echo "gcov was not found, skipping coverage check"
	fi
else
	echo "Not on a Linux node, skipping coverage check"
		
fi

if [[ "${JOB_NAME}" == khmer-multi/* ]]
then
	if [[ -x ${cov_analysis_dir}/${cov_analysis_bin} ]]
	then
		if [[ -n "${COVERITY_TOKEN}" ]]
			#was -v COVERITY_TOKEN, but OS X bash not new enough
		then
			PATH=${PATH}:${cov_analysis_dir}
			coverity="${cov_analysis_bin} --dir cov-int"
		else
			echo "Missing coverity credentials, skipping scan"
		fi
	else
		echo "${cov_analysis_bin} does not exist in \
			${cov_analysis_dir}. Skipping coverity scan."
	fi
else
	echo "Not the main build so skipping the coverity scan"
fi

${coverity} python setup.py build_ext ${coverage_post}

if [[ -n "$coverity" ]]
	# was -v coverity but OS X bash not new enough
then
	tar czf khmer-cov.tgz cov-int
	curl --form project=Khmer --form token=${COVERITY_TOKEN} --form \
		email=mcrusoe@msu.edu --form file=@khmer-cov.tgz --form \
		version=0.0.0.${BUILD_TAG} \
		http://scan5.coverity.com/cgi-bin/upload.py
fi

pip install --quiet nose coverage
./setup.py develop
make coverage
# we need to get coverage to look at our scripts. Since they aren't in a
# python module we can't tell nosetests to look for them (via an import
# statement). So we run nose inside of coverage.

make doc

pip install --quiet pylint
make pylint

if [[ -n "${coverage_post}" ]]
	# was -v coverage_post but OS X bash not new enough
then
	pip install -U gcovr
	# work around a bug in 3.1 ?
	# pip install -e  git+git@github.com:nschum/gcovr.git@fix-argument-type#egg=gcovr
	# gcovr -r $PWD --xml > coverage-gcovr.xml
	gcovr --xml > coverage-gcovr.xml

	make cppcheck

	make doxygen
fi