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#!/bin/bash
type module >& /dev/null || . /mnt/software/Modules/current/init/bash
module purge
module load gcc
module load ccache
module load python/3
module load htslib # since pysam was built against this
#module load make
set -vex
which gcc
which g++
gcc --version
which python
python --version
export PYTHONUSERBASE=$(pwd)/LOCAL
export PATH=${PYTHONUSERBASE}/bin:${PATH}
PIP="pip --cache-dir=$bamboo_build_working_directory/.pip"
if [[ -z ${bamboo_repository_branch_name+x} ]]; then
WHEELHOUSE=/mnt/software/p/python/wheelhouse/develop
elif [[ ${bamboo_repository_branch_name} == develop ]]; then
WHEELHOUSE=/mnt/software/p/python/wheelhouse/develop
elif [[ ${bamboo_repository_branch_name} == master ]]; then
WHEELHOUSE=/mnt/software/p/python/wheelhouse/master
else
WHEELHOUSE=/mnt/software/p/python/wheelhouse/develop
fi
export WHEELHOUSE
rm -rf build
mkdir -p build/{bin,lib,include,share}
# Delete avro.
# avro-python3 would work, but avro must be deleted no matter way.
# https://stackoverflow.com/questions/40732419/how-to-read-avro-files-in-python-3-5-2
rm -rf ${PYTHONUSERBASE}/lib/python3*/site-packages/avro*
pip install --user --no-index --find-link "${WHEELHOUSE}" --no-compile -e '.[test]'
make test
##########################################################################
bash bamboo_wheel.sh
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